LONG-WINDED INTRODUCTION
Let's be serious, the Star Wars prequels weren't exactly everything we had hoped for. There were a lot of reasons for this: One is that we're no longer seven or nine years old like we were when we first saw the original films, and thus weren't as able to overlook the glaring flaws in the prequels like we used to do with the older movies. Another is that the driving factor of the prequels was toy sales and technological breakthroughs, so that the emphasis shifted to effects sequences, props, and costume changes rather than story. Another is that George Lucas hadn't directed a film since 1977 and hadn't written one since 1989, so, y'know, dude really didn't know what he was doing. Another is that Lucas was rich and had kids and was completely secure by the time he made the prequels -- that is, he didn't have to risk himself artistically and had no angst or passions left to express. And last but not least, the prequels followed a plot outline that -- while it produced commercially viable movie stories like Episode I -- didn't really mesh up with what had been said (or implied) in the original movies. Anakin built C-3PO? Obi-Wan first met Anakin as a child? Boba Fett is a clone of a boring New Zelander who can't act? Etc. Not to mention the way the prequels shamelessly copied plot elements from the original movies for no reason other than to stretch out the running time with action setpieces. Ah, the primitive Gungans defeat the droid army of the Trade Federation in a battle of nature vs. technology? Reminds me of the finale of Return of the Jedi. Oh look, a chase in an asteroid belt! Just like Empire Strikes Back. Hey! The fighters have to blow up the big space station by hitting it in a specific spot to blow up the main reactor and the hero does it by a great fluke? I think I'm seeing double! Etc. etc. Lucas calls this trying to draw attention to the cyclical nature of mythic sagas, I call it laziness and a desire to keep things familiar.
All those things considered, if I'd been in charge with plotting out the prequels, I would've handled things a little differently. Of course, that would've never happened, I was after all just a kid when the damn things were being made, but still. Also, Lucas stays on as Executive Producer, story consultant, bankroller, big boss, etc. -- but not writer/director. The best two Star Wars movies were written by Lawrence Kasdan and directed by other people (Irvin Kersher and Richard Marquand). JJ Abrams should've directed one instead of ruining Star Trek, for example. But when you've decided to shoot completely digitally with no sets, no locations, just the actors, green screen, and half the characters played by tennis balls, all of a sudden you've taken away all the things that help actors act; especially young and inexperienced actors like Hayden Christiansen and Natalie Portman (you may notice Chris Lee and Ian McDiarmid do fine, this is because they're also experienced stage actors). And when an actor has nothing to work with and is floundering, that's when you need a good director. Lucas is an exceptionally talented creator, with an amazing imagination and eye -- but he is notorious for being poor with actors. On the first Star Wars he was helped because there was spectacular costumes and production design and sets RIGHT THERE for the actors to work with, and the main three (Hamill, Ford, and Fisher) have remarked that having experienced actors like Alec Guiness and Peter Cushing on set to look up to helped immensely. On Empre and Jedi, which feature all-around better performances from the entire main cast, there were different directors. So yes, Lucas is an essential part of making those prequels, but by God he should've found other directors.
That being said, here's how I would've plotted out the prequels.
EPISODE I: THE PHANTOM MENACE (<-- it's a great title, let's keep it)
We can begin with Qui-Gon and Obi-Wan, just like the filmed version. Yes, Qui-Gon wasn't even hinted at in the original trilogy and Obi-Wan flat out says in Empire that he was trained by Yoda, but Qui-Gon is pretty good storytelling tool in that he gives us an older mentor Jedi character to contrast a younger Obi-Wan too (let's keep Yoda limited to being a largely sedate puppet, shall we?). So let's say that Qui-Gon is just that, a mentor character to an Obi-Wan who is already a young Knight himself, but not exactly Obi-Wan's "Master". It's about thirty years before "Episode IV: A New Hope" and Obi-Wan is perhaps thirty-two years old (as opposed to 25 in the filmed version).
The biggest problem with Episode I as I see it is the entire Naboo plotline and Trade Federation enemy. It's ultimately just an excuse to move the characters forward, a massive mishandled maguffin if you will, and consists either of boring dialogue scenes between a deep-pitched fourteen year old girl and badly executed puppets based on outdated racial stereotypes, or rip-offs from other parts of the story (land battle in Jedi plus the space battle in Star Wars). The one thing that maybe would've made us care about the storyline, that is actually seeing the suffering of the people under the blockade, is never shown. The other big problem with Naboo is that it contributes nothing to the rest of the trilogy. The trade federation never really amounts to anything, other than contributing nice, safe, bad guys for us to kill in the other two movies. So get rid of it. Ditch the Naboo plotline. (Notice this also eliminates the film's most hated character).
In my version, Qui-Gon Jinn (still an unorthodox rebel and opponent of the Jedi Council) suspects that something is rotten in the proverbial state of Denmark. He suspects a great corruption in the Republic and seeks to unravel it, and brings Obi-Wan with him as he sees much promise in the young Jedi who is idealistic and ready to serve. In essence the journey they take is the one Obi-Wan goes on in the filmed Episode II. Qui-Gon follows a series of clues through the galactic underworld that someone in the Republic is funding a vast project, like say the creation of a clone army. Turns out the Republic has been in trouble for a while, with economic disparites and so on between the Core Worlds and the Outer Rim creating dissatisfaction. Enter Count Dooku, who in this version has nothing to do with the Jedi or Sith, who is a wealthy Core World aristocrat using this disaffection to his ends. Qui-Gon and Obi-Wan encounter evidence that Dooku is paying someone a ton of money to create an army that he could use to rally the dissatified systems into succeeding and thus sparking a civil war.
One of the planets they visit in this trail of clues is Tatooine, an Outer Rim world on which Dooku's propaganda holds much strength. In their dealings with a grizzled human junkdealer (essentially Watto) they meet his slave housekeeper Shmi Skywalker and her son, Anakin. Anakin is 15 years old here, as opposed to the 9 year old of Lucas' version. Here Anakin is petulant and headstrong, and spends what free time he has racings swoops in illegal street races that "Watto" makes money betting on. He is unusally good. Qui-Gon senses that the Force is strong in him, and Shmi confides in him that he "has no father". We keep the whole immaculate Force conception angle for its mythical resonance, although for adults in the audience we also throw in implications that our now human Watto could just as easily be the boy's true father. Qui-Gon believes this young boy could be trained into a great Jedi, but is unable to take him away because he is a slave. When Watto leads them to a source that takes them off Tatooine, Qui-Gon and Obi-Wan leave the desert world and Anakin behind.
They finally end up on Kamino (or Spaarti or Mandalore or wherever you want the clones to be from. It doesn't really matter). There they meet the clonemakers and discover that an absolute massive clone army is in fact being grown for Dooku and the secessionists. Qui-Gon manages to stop the clonemasters from creating more on the grounds that their action is treason against the government, but Dooku shows up and manages to take possession of the majority of the clones already grown/trained. A battle ensues between the Jedi and Dooku's forces for control of the clones, with a small number of the clones (say, 1000-10,000) being left behind as Dooku escapes with the majority (several hundred thousand, possibly a million). By the way it doesn't matter who these clones originated from, and at no point does Jango Fett ever show up. To destroy the Jedi and make sure they never reach Coruscant to inform the Senate, Dooku leaves behind the Sith warrior, Darth Maul, who can remain relatively unchanged. Maul battle Qui-Gon and Obi-Wan, Duel of the Fates music, Maul kills Qui-Gon, Obi-Wan kills Maul, pretty much as filmed.
Obi-Wan makes it back to Coruscant and informs the Senate of all that has transpired and presents the evidence of the clone army. Turns out that Dooku and the seperatists have already announced their intentions and formed the Confederacy. The war has, in effect, already begun. However, since the Republic has been the sole galactic government for over a thousand generations, it lacks a standing army with which to combat this threat. Intrigued by the news that a small amount of trained clones remains on Kamino, the ambitious and wily Senator Palpatine proposes using them to form the backbone of the Republic Army in order to combat the Seperatists. Chancellor Valorum opposes the notion, as he is unsure of the ethics of using the clones in such a way (are they people, etc etc). Palpatine accuses Valorum of weakness in a desperate time of action, vote of no confidence, is nominated and wins the Chancellorship based on the platform of restoring unity to the Republic.
Meanwhile, Dooku makes it back to his retreat where he meets with his master, a mysterious hooded figure called Darth Sidious.
EPISODE II: ATTACK OF THE CLONES (<-- this title makes sense now)
It's about three or four years later. The Clone Wars rage throughout the galaxy and so on. People are dying, things are bad. The Republic controls the clonemaking facilities on Kamino, meaning that their army is constantly on the grow -- its largely a small but growing elite of clones with a large recruited force of Republican patriots. The Confederacy is the opposite -- no longer in possession of clonemaking technology, they've had to conscript. Their army is largely made up of cloned soldiers, but has a small growing class of poorly trained enlisted fighters. Officers in both armies are non clone, of course.
Into this back-drop we rejoin our hero, Obi-Wan Kenobi. He, along with the other Jedi Knights, once protectors of the Republic, has been made a General of the Army. The film opens with Kenobi fighting alongside Senator Bail Organa, Viceroy of Alderaan, defending the planet which is under attack from Confederate forces. This is primarily an entrenched land battle, with Confederate clone jetpack troopers fighting the Jedi and Organa's forces. Ultimately, General Kenobi comes up with a brilliant strategy winning the day, earning the friendship and respect of Organa, as well as gaining him some hero status in the Republic, since they are generally losing the war to the better armed Seperatists.
Kenobi, generally a private person, has no wish to be a hero. He doesn't much like Chancellor Palpatine, who he sees as an oily opportunist, and has never been comfortable with the way Palpatine has used the war for personal and political gain. When Kenobi confides his discomfort in public appearances to Palpatine, the Chancellor suggests that if Kenobi does not wish to be the hero, he should find someone who does.
With things approachng desperation and the war reaching a critical stage, Kenobi returns to the Outer Rim world of Tatooine to try and find out what has happened to young Anakin Skywalker. Kenobi thinks that the boy, trained as a Jedi, could be a great help in the war effort. Upon his return, Obi-Wan discovers "Watto" sold off the Skywalkers years ago to pay off his debts, to a moisture farmer named Cliegg Lars. Kenobi makes his way out to the Lars homestead, and learns that Lars freed the Skywalkers and married Shmi, raising Anakin alongside his own son Owen. Shmi has died in the years since and Anakin himself has become impatient, disobedient, and sullen. He does not like moisture farming. He misses speed and thrills, and craves adventure. Owen, meanwhile, sees Anakin as immature and naively idealistic. To Owen, Anakin's right place is with him, helping out on the farm and making money to improve their station in life. Owen sees the Clone Wars as something very far off and unaffecting, and to Owen it doesn't really matter if the Republic wins or loses. To Anakin it is everything. Anakin thinks of Dooku as nothing but an opportunist and a liar, and respects the Republic because it brings order and control to the chaos of the galaxy. Anakin venerates the Jedi. He has always dreamed of being a Jedi ever since he met Qui-Gon and Obi-Wan. So the return of Obi-Wan is a huge event for him, and Obi-Wan hardly has to do any convincing to get Anakin to leave the farm and join the war.
Obi-Wan immediately begins training Anakin as a Jedi, although he does not have initial approval from the Jedi Council to do so. While Kenobi tries to get Yoda to recognize the potential in Skywalker, Anakin enlists in the Republic Starfighter Corps, showing immediate skill and promise. Intelligence leaks to the Republic that there will be an opportunity to capture Dooku on the banking planet of Muunilinst (or somewhere, its really not important). Kenobi is suspicious, since Dooku has been elusive since the war began and it seems unlikely that this is not a trap. Nevertheless General Kenobi is ordered to command the ground assault, and Skywalker is part of a squadron of starfighters running interference against the Confederate capital ships in space. During the space battle, the Republic fighters are nearly massacred due to their use of old and outdated tactics against the more savvy Confederate flyers. After the senior pilot officers are killed, Skywalker ends up taking command of the remaining fighters, building a makeshift squadron amongst the remnants of the shattered Wing. Turning the tide thanks both to his incredible piloting skill and intuitive/innovative tactics, Skywalker manages to win the space battle for the Republic, effectively destroying Confederate space suppor/Dooku's ability to escape, impressing the younger pilots especially.
On the ground, Kenobi manages to defeat Dooku's forces thanks to the advantage of the loyalty and skill of the Republic clonetroopers and regular forces over Dooku's more patchwork army. Eventually Kenobi pursues Dooku into a key structure to capture him personally, but Dooku manages to evade Kenobi and trap the Jedi General in some kind of 1940s serial style deathtrap. Dooku escapes to his private shuttle, where is suprised to find Darth Sidious waiting for him. The mysterious cloaked figure tells Dooku that there is no need for his escape. Dooku is initially pleased, assuming Sidious is implying the Republic space forces were defeated and reinforcements imminent. Instead, Sidious merely informs Dooku that he has "outlived his usefulness" and unleashes Force lightning upon him, killing him in a horrible display. Sidious then destroys Dooku's shuttle. Kenobi is rescued from the death trap by Skywalker, who arrives in the nick of time (of course) to save his master. The two hurry up to Dooku's shuttebay, but find only an exploded shutte and Dooku's charred corpse. Anakin assumes that the shuttle somehow malfunctioned and Dooku's death was accidental. Kenobi insists that it looks too planned, and believes the act was "suicide".
Upon returning to Coruscant, Anakin is pleased to find that he has been recognized by the Jedi Order as Kenobi's apprentice, and both Jedi are decorated by Chancellor Palpatine for their part in helping to bring the War to a close. Palpatine notes, however, that the seperatist threat is still extent, and that there is much mopping up action necessary before peace can be achieved.
EPISODE III: REVENGE OF THE SITH (if you want a new title, the best option I think was RISE OF THE EMPIRE)
Again, we've jumped forward three, maybe four years. Mopping up actions for the Clone Wars have slowed to a crawl, with the Republic now possessing a vast number of elite clone troopers in addition to regular armed forces and highly skilled officers. The entire system has slowly become more militarized and controlled. One hold-out Confederate General remains, we can call him Grievous if we like, out on an Outer Rim world like say Utapau if we must. He leads a ragtag force of volunteers, mercenaries, and war droids.
Former General and war hero Obi-Wan Kenobi is upset with the continuation of the war, believing Grievous to be of no threat and Palpatine to merely be continuing the situation to grab more power. Kenobi has become very suspicious of the good luck that presented the Republic with the clonetroopers at the start of the war and allowed Palpatine to grab the Chancellorship, and has begun looking into the Chancellor's dealings. Meanwhile, he has begun using the name "Ben Kenobi" and attempting to stay out of the spotlight and distance himself from his wartime persona.
His promising young apprentice Anakin Skywalker, on the other hand, has gone on to become a famous war hero and a full Jedi Knight, achieving a high rank and numerous honours during the Wars. Anakin has somewhat drifted from his former mentor, he believes that Grievous is worth going after, as are all threats to the security of the Republic. As a decorated and respected hero, he has also become the target of the Chancellor's friendship. Palpatine takes Anakin to aristocratic social events and functions, and indulges him with political and personal favours. During one of these social gatherings Anakin is introduced to Princess/Senator/Countess/Whatever (actually I like Countess best, but anyway) Padme Amidala, a politically active young woman, five years Anakin's senior, whom he is smitten with immediately. He begins trying to court her, and is tremendously clumsy at it at first. She's unimpressed with the war hero, and only begins falling for him when he opens up more about his true feelings. AKA Big Romantic Subplot. The essential bones of it is that she warms to him, he charms her, she's impressed by his commitment to the Republic, which she feels is being torn apart, and it does not matter if they get married or not. Maybe they elope, maybe its a secret wedding, maybe it never happens. But the point is that she gets pregnant. And the bigger point is that he has NO IDEA that she gets pregnant, because he's busy with the rest of the plot that will be occurring. At some point during this subplot Anakin introduces her to Obi-Wan and they like each other and become friends.
Anakin meanwhile is drawn closer into Palpatine's inner circle. Obi-Wan and Padme, who both distrust Palpatine, hope to use Anakin's friendship as a means of discovering more about the Chancellor. All in all these bits can be very similar to the filmed product, which did a fine job of Anakin and Palpatine's developing relationship and Palpatine's role in corrupting him. In my version however, Anakin would've been more and more attracted to Palpatine because of Palpatine's commitment to order and defending the Republic. Drawn closer into Palpatine's inner sanctum, Anakin eventually learns the Chancellor's hidden secret: that he is in fact Darth Sidious, the last remaining member of the Sith, a group of evil Dark Jedi thought defeated a thousand years ago, and has been searching for an apprentice ever since the loss of Darth Maul at the beginning of the war. However, Palpatine has so seduced Anakin that Skywalker isn't really bothered by this revelation. From his experiences in the war he finds he no longer recognizes much difference between the so-called light and dark sides of the Force, since both kill to achieve their aims, and is merely pleased to discover that the defence and safety of his beloved Republic is in the hands of a skilled and powerful Force master. He does, however, understand that Palpatine can teach him much that was previously forbidden, and that will help Anakin to grow in power and prestige in the political circles and military circles he now moves in. He agrees to begin learning dark side secrets from Palpatine. At this point he adopts the name Darth Vader.
Meanwhile, General Kenobi's comission has been re-activated by the Chancellor's office and he has been sent to Utapau to root out Grievous. Kenobi recognizes that this has been done solely to get him away from the capital and his investigation, and most probably to get him killed. However, Kenobi goes regardless and does battle with Grievous' forces. Upon confronting Grievous in single combat, Kenobi learns the truth -- it was Palpatine, under the guise of Sith Lord Darth Sidious, who in fact ordered the creation of the clone army. The entire war was simply Palpatine's solitary chess game. Fearful for his life, Kenobi finds that the clonetroopers under his command have turned against him -- as they are ordered to do against anyone who discovers the truth. Ben barely makes it out alive and immediately heads to Coruscant to warn Anakin.
He arrives to find Anakin and Palpatine together, and it is clear who has sided with who. Kenobi confronts Palpatine and tries to sway Anakin from his side, and the two duel. This is similar to the Mace Windu scene in the film, only Palpatine never fights and Kenobi has replaced Windu. Anakin defeats Kenobi but is unable to kill him, and Kenobi makes good his escape. Palpatine makes the assault public, and convinces Anakin and the public that is in fact the result of a consipracy of the "power-hungry, outdated Jedi Order" against him. The clonetroopers turn on their Jedi commanders, and we get the Order 66 sequence essentially verbatim, right down to Skywalker personally leading clones on the Jedi Temple and burning that shit down. Palpatine uses the emergency to declare himself Emperor, placing all military forces under his direct control so that "order and stability may be restored."
At this point Anakin is convinced that Obi-Wan has betrayed him and that Palpatine is the only one he can trust. Kenobi convinces Padme that its all over, and that the only alternative now for her safety and the safety of her unborn children is to escape Coruscant. Its clear now to Padme that Anakin is not the man she loved, and has become Palpatine's pawn. Kenobi takes Padme to escape, planning to regroup with Yoda later.
Yoda, who has been present up until this point as a subtley done puppet, the wise leader of the Jedi Order, confronts Palpatine. They fight. This is the only time Yoda or Palpatine fight. It's a powerful duel and doesn't devolve into such silliness as throwing Senate platforms at each other. Palpatine wins, but Yoda manages to escape.
Anakin pursues Kenobi to the lava planet Mustafar, where Kenobi is forced to stop for repairs. Seeing Obi-Wan and Padme together infuriates Anakin -- he believes he knows now what has been going on. He attacks Padme, and while Obi-Wan manages to save her, she is left unconscious aboard the ship. Anakin and Obi-Wan's duel continues outside, and is totally awesome, Battle of the Heroes music, but the fight choreography is 100% less silly. Ben has the high ground, Anakin gets chopped up into little bits, crawls up from the pit and lights aflame, Obi-Wan leaves him to die and takes off with Padme.
Obi-Wan meets up with Yoda on Dagobah, who has brought Bail Organa. Organa recognizes the evil that has spread through the Republic, and knows that Palpatine's Empire is merely the culmination of it, not the cure. He agrees to help Kenobi due to his great respect for his wartime service. The twins are born on Dagobah, and Yoda and Obi-Wan agree to seperate them for their safety. Organa takes Padme and the girl, Leia, into his care on Alderaan. Obi-Wan takes young Luke back to Tatooine to be raised by his uncle Owen.
Palpatine has Anakin reborn into Darth Vader, more machine now than man, and charges him with the task of wiping out the remaining Jedi.
No cheesy shot of a half-built Death Star, in fact no mention of the Death Star at all. No Jango Fett, no Boba Fett. No Threepio and Artoo. No Mace Windu. No Nute Gunray. No Jar Jar Binks. No crying Padme scenes, no Padme dying for no reason, Anakin's turn is not motivated by love but by desire for power.
And that's how I see it. The trick to it all is that Anakin is Goering, and Palpatine is Hitler, essentially. Basically EPISODE II becomes EPISODE I, EPISODE II gets the Clone Wars, and EPISODE III remains largely intact but with the time consuming Clone Wars elements largely removed and the character motivations changed around.