This is going to be a long post. Mainly due to the heavy nature of the subject but also because it was a slow night at work.
George Lucas has declared to the world that he is going to be rereleasing  all 6 Star Wars films in order and this time in 3D. This is more or less an open invitation for the Internet to let loose with both barrels about how this will ruin/improve the movies in the charming way that that they tend to do whenever anyone makes an announcement like this.
He's left himself a loophole by saying that each film will be released a year apart starting with Episode 1: The Phantom Menace and this is a flop then the project will be canceled and never spoken of again.
This means that everyone can breath a sigh of relief because Phantom Menace is never going to be counted amongst the greats of cinema
My own theory is that he has spent so much time at the top of the world and nobody is willing to tell him “No”
Back when he was a young and hungry film maker people said “No” all the time.
“No you can't film like this” “No these films will never work” “No you can't have another slice of chocolate cake”
Determined to prove them wrong he pioneered new camera techniques and in making Star Wars he pushed all sorts of envelopes in all sorts of directions. Now in all fairness he still pushes the boundries of what can be done but now that he depends so much on the computer departments skills it has cost him in the humanity that actors project into their characters. Don't get me wrong, they still do the job well but nobody in the prequels really gives off an air of confidence in their role, the believability just isn't there.
Personally I think that when he decided to finally release the prequels he should have have invested some time on his old 16mm cameras, perhaps even going so far as releasing a black and white film and labeling it as “Art house”
This would have reminded him of the old days when it was just him and a small crew that nobody thought was ever going to get anywhere. Thus, armed at at last with the proper mindset, he would have been able to tackle the prequels. 
So without further ado I present my suggestions for improving the plot of Star Wars, which you could compare to rewriting Shakespeare but only if you were prepared to withstand the thespianic onslaught of Crazed Caliban, Outraged Oberon and Mad Macbeths “Curse this” Paratroop brigade
Episode 1: The Phantom Menace
- Basic Story:
2 Jedi, Qui Gon Jin and Obi Wan Kenobi are sent to Naboo to negotiate a blockade that the Trade Federation have put in place. They are ambushed and make their way down to the planet just in time to catch the invasion.
Escaping with the Queen they crash land on Tatooine where they meet Anakin Skywalker, a slave.
With the help of some fancy flying Anakin is freed and taken with the them to become a Jedi. The blockade of the trade federation is broken and its leaders captured.
- What needs to change:
Anakin Skywalker - For a slave he was just a little too happy.  Considering what is going to happen to him he needs to be kicked around by life a little.
Darth Maul - Instead of being killed off at the end of the movie he should have been rescued by Palpatines minions  and slowly rebuilt into General Grievous.
Padme Amidala - She was incredibly wooden. Perhaps she was attempting to display royal austerity but a little bit more emotion on her part would have gone a long way.
Jar Jar Binks - An enormous amount of potential lies in this character  but the main problem was that he was supposed to be the annoying cute thing. Then they tried to make him the comedy sidekick but that failed at all levels except for the most basic.  What he really needs is a slightly tamer role of sidekick and also the displaying of an ability that he is able to do with confidence.
Episode 2: Attack of the Clones
Obi Wan Kenobi and his padawan Anakin Skywalker are detailed to protect Padme Amidala who has been targeted for assassination. In his investigations Kenobi discovers a clone army being built for the republic. He informs the Jedi Council and finds that Count Dooku, a former Jedi turned Sith, is the leader of the growing separatist movement and his captor.
Anakin and Amidala rush to rescue him but are captured themselves. Just as it seems all hope is lost the clone army suddenly appears. Dooku fights everyone with a lightsaber and then runs away.
- What needs to change:
The Growing Arrogance of the Jedi - Mace Windu, Kenobi and Yoda have a slight discussion about it and in the bar scene Anakin displays a small touch of it but aside from that there really is no feeling that the Jedi are growing more arrogant.
Padme Amidala - Still teams up with Anakin to investigate the fate of Kenobi but ends up falling for Kenobi rather than Anakin.
Count Dooku - He is still the main bad guy and the apprentice of Palpatine. But he is planning to take Palpatines place and has an apprentice of his own, the twisted wreckage of the thing that was once Darth Maul, which is now a cyborged mockery of what it used to be.
Shimi Skywalker - Still taken by Sand people but not kept alive for no apparent reason this time  Anakin still slaughters them and turns to Padme Amidala for comfort which she gives but as a close friend. It is only in Anakins mind that the gesture is meant as something more.
Darth Maul - At the very end of the movie, even after the credits, we see the systems finally come online and the cyborg steps out of the construction bay with much snapping of wires. A fury filled cry fills the air and the camera rises, playing with the light so that it teases the audience and offers only the slightest clue as to who or what this thing could be. 
Episode 3: Revenge of the Sith
The war rages on between the Separatists and the Republic. Palpatine emerges as the emperor and rides a wave of public support against the Jedi who are ruthlessly exterminated .
Anakin Skywalker turns to the dark side and kills everyone but is defeated by Kenobi. Luke and Leia are born.
- What needs to change:
Padme Amidala - She has married Obi Wan Kenobi in secret and is now pregnant.
Anakin Skywalker - Eaten alive by jealousy at Kenobi and Amidala, he goes before the Jedi council demanding to be recognized as a full fledged Jedi Knight. He is rebuked because it is Kenobis place to put him forward.
He then goes to Kenobi and threatens to reveal his secret marriage to the council but Kenobi refuses because he, rightly, feels that Anakin is not emotionally ready for the trials.
Finally Anakin goes to Palpatine, who has always been a father figure to him, he reveals that the Jedi Council have refused to recognize him as a Jedi Knight and also that Padme Amidala and Kenobi are together. Palpatine easily convinces him that Padme would want to be with him if Kenobi were not around.
Darth Maul - Operating under the name, General Grievous. He is a tactical mastermind against the Jedi. When Kenobi tracks him down it is revealed that he no longer has access to the force and instead has a range of droid abilities allowing him to replicate this. However it is not enough and Maul is forced to retreat or be destroyed.
Obi Wan Kenobi - After coming face to face with General Grievous who is revealed to be the cyborged Darth Maul Kenobi receives word that Amidala has been abducted. Analysis of the evidence reveals that it was Anakin Skywalker who took her.
With the assistance of Yoda who knew about the marriage the whole time but didn't say anything he tracks Anakin down and they begin the final duel. At the end of the fight Kenobi has to make a decision on who to save, Anakin or Padme. He chooses to save Padme and leaves Anakin for dead on the surface of the planet, but he is too late to save her life as she delivers the babies. The children are split up to prevent for their safety. 
Yoda - After assisting Kenobi on his way he makes his way to the senate buildings to confront Palpatine about his handling of Anakin. Palpatine attempts to bluff his way out of it at first but it ends up with a climatic duel between Jedi and Sith. Eventually Yoda is badly wounded and escapes. Palpatine uses doctored footage of the fight and pure propaganda to turn the tide of public opinion against the Jedi. The clone armies are ordered in. 
Count Dooku - With his usefulness s at an end he is discarded by Palpatine. He moves into hiding quickly to avoid being captured or killed. The attacks on the Separatist movement increase and he realizes that he has been played for a fool this whole time. He swears vengeance on Palpatine.
Episode 3.5: Final Stand of the Jedi 
There is an epic three sided war being fought across the galaxy. On one side is the Republic, led by Senator Palpatine. Although it is not yet the Empire it is starting to show signs of what it will one day become.
The second side is the Separatist Movement, led by Count Dooku, he has abandoned Palpatine but not the Sith teachings.
Finally there are the Jedi who are led by Master Yoda, they are the smallest side and, for the most part, are fighting simply to stay alive.
- Character Motivations:
Anakin Skywalker/Darth Vader - Has discovered that Padme is dead and blames Kenobi for it. He hunts Kenobi with a passion in an effort to find the children that, in his madness, he believes are his. It is on this hunt that he makes the necessary bounty hunting connections that will serve him well in later years. 
Obi Wan Kenobi - Is hunting General Grievous/Darth Maul because he has proved to be an outstanding general that has managed to decimate the Jedi forces. Although he doesn't want to admit it he also seeks revenge for the death of Qui Gon Jin, something he has never really gotten over.
Yoda - Is number one on the hit parade and on the run from almost everyone. He fights off bounty hunters and clone troopers alike until he comes to Dagobah. The planet is extremely wild and very dangerous and after his own vision quest at the dark side tree  he stays there quite safe and quite alone.
Count Dooku - Divides his time between leading The Separatists and searching for ways to destroy his former master and his new apprentice.
Jar Jar Binks  - At the start he is living happily in the Republic. He has money and power. But when he discovers something big  his eyes are opened to the reality of what he has helped to bring about and he escapes.
He finds few friends amongst the Jedi Order as they see him little more than the architect of their misfortunes  It is conceivable that he be given a cameo appearance in “A New Hope”  as an officer of the rebel alliance. But if this happens we can expect that he would have been kicked around a lot during the war and he would now be confident in handling his weaponry. His character to be very much changed from the years spent fighting the war. 
- Specific Plot Points
The death of General Grevious/Darth Maul - In a deserted separatist base Kenobi and Vader reluctantly work together and Darth Maul is finally defeated once and for all. But Kenobi is badly wounded in the fight and Darth Vader takes the opportunity to torture the information about the location of the children out of him. Kenobi is strong enough to give him false information but the effort of doing so saps his strength and will almost utterly.
Darth Vader leaves him clinging to the last few breaths of his life in a moment of irony that is too good to pass up and just as it seems that things are at their darkest the ghost of Qui Gon Jin appears to take care of his apprentice.
Kenobis fate - Disillusioned with the war Kenobi leaves the tattered remains of the Jedi Order. He feels that all that has happened is his fault and has had enough of the war. In secret he moves to Tatooine in order to keep an eye on the young Luke Skywalker. 
The attack on Palpatine - Using his contacts inside the fledgling imperial center Count Dooku infiltrates the palace and fights with his former master. Although he loses it is a noble death and he is the one that scars Palpatine so very badly.
- And in some cases Re re releasing.
- He could also have hired the biggest Star Wars Geek he could find and use him as a sounding board for his ideas.
- We've gone over the minion thing before. You try and take over the universe without minions and see how far you get.
- I know that to say anything other than “he should have been killed off quickly” is grounds for being thrown out of an airlock while in hyperspace but bear with me on this.
- But they overlooked the fact that Anakin Skywalker already had this part down pat
- Prat falls and not much else
- All we've ever heard about Sand People is that they are so very dangerous and yet here they are conveniently keeping her alive. Damn you Lucas!
- This reveals that the technology necessary to do this sort of thing exists. The Robotized Darth Maul is essentially the prototype Vader.
- And, I would imagine, in need of a doctor. But who?
- "Lets name him after the dark lord of the sith" "Yes lets!"
- Something that needs to be shown is the Jedi orders increasingly futile attempts to keep a lid on this situation that is rapidly spiraling out of control.
- Yeah it's a new movie. There's now so much stuff unresolved that you get an extra movie out of it. If Joss Wheedon were taking notes then perhaps we'd all be watching Serenity 2: River Tam beats up beats up even more Space Cannibals.
- Possibly he could come into conflict with Palpatine over the time he is spending on this hunt. This would contrast nicely with Count Dooku allowing General Grievous/Darth Maul more or less free rein
- And who wouldn't want a look at a Dark Yoda?
- Yes he's still alive. Don't look at me like that
- He'll be investigating some discrepancies in the finances and come across the Death Star expense account.
- He was manipulated, fairly easily, by Palpatine into proposing that the chancellor be given power overwhelming.
- Even if this means we'll have yet another release of all the films.
- He can still die horribly if you want. All it means is that this time it would be for a purpose not just because he was some annoying toad thing.
- Seriously? Did Vader even bother looking in the Galactic Phonebook?