I'm new here. I've been obsessively reading this thread, though, because I've really wanted to fix these movies for a long time.
Three main ideas:
1. Anakin is the "droids" of the prequels. What do I mean by this?
In the original Star Wars, 3PO and R2 were the perspective characters, based on a duo of peasants in the Hidden Fortress who observed the action. Most of the opening is spent on them, and their wandering through the desert has a surreal, wondrous, almost art film quality before they meet Luke.
I think Episode 1, starting off not only a new film series but the entire series, should have a similar character. I think this character should be (an obviously much more quiet) Anakin. This fits in with R2 being, as Ben Burt described, a sort of toddler. He's childlike and takes things in from a distance, helping out when needed. This also works as foreshadowing, for him becoming more machine than man.
The film could start off on Tatooine, with Anakin going through a normal day and running into something much larger than himself. He would be beneath the notice of everyone until after the podrace. He need not have actually built the podracer, but he could be a podracing fan and an amateur tinkerer and student of mechanics who does much, much better once Qui Gon teaches him to tap into the Force. This "opening" also has parallels to Luke having work to do at the beginning, except that Anakin is literally enslaved, which garners more sympathy.
2. Totally Radical Changelings
So, the opportunity for a changeling to do something interesting in Episode 2 was completely shot, except for being able to use a line about it.
With all the ideas about Grievous transforming into Maul, Qui Gon being Dooku, Palpatine hiding his true appearance, the identity of Darth Vader, and so on, I decided to try and make them all into something cohesive.
The Jedi rely a lot on Eastern philosophy and religion. Why not incorporate something else? Namely, reincarnation.
So, in this new prequel universe, one of the uses of the Force, particularly for its most powerful adherents, is to become a changeling. Becoming a changeling allows you to reincarnate. This is how Yoda has lived 900 years, how Palpatine is an ancient evil, and where Force ghosts come from. Midichlorians can stay (yay! :D) as the kind of cells that rebuild your body after its passing, so Anakin having them (and comparing his amount to Yoda's) actually means something.
However, if you are evil, and your soul is corrupted, you require machinery to preserve your new body.
Prime examples: Qui Gon, after his death as a renegade but a good guy, is reincarnated into Dooku, no machinery. Darth Maul is a changeling who is reincarnated as General Grievous, the "droid general." Palpatine tempts Anakin with the idea that he can give Padme this reincarnation (perhaps giving up his own, making it seem more plausible,) which is already established at this point, and he is clearly a master of it. As proof of concept, perhaps Palpatine manipulated Dooku into giving his reincarnation to Jango, turning him into Boba, which also explains why his ghost doesn't show up after he dies.
This provides additional reasons for why a clone army would be so valuable in this time of shifting identities: they're all exact copies of non-Force people, so they can't change alliances after they die.
To preserve the surprise of Darth Vader's identity, you could give all changelings some sort of "tell" that differentiates them from other people (maybe a ring or a twinkle, nothing too serious,) and give the newly-suited Vader this quirk, letting the audience know that this is someone else who has come back, and telling them to keep an eye on him to try and figure out who he is. Since so many bad guys have died, he could be any of them. Anakin actually dies at first.
This also means we don't need to do complicated work trying to turn actors into other actors. Just reincarnate them, like in Doctor Who.
3. Padme is a warmonger.
It's way more interesting that way. Just cut out some stuff, and she's a war hawk for the Republic, spurring Anakin on until she realizes the problems of her actions. Combined with the reincarnation idea, this adds some tension - the audience knows she's not pure enough for it to work, as much as Anakin believes. The Queen keeps decoys because she's paranoid. The Queen attacks the Federation head on and takes down Valorum because she's headstrong. Padme accepts Anakin's genocide, because she might have done the same in his position. Padme quips about diplomacy with sarcasm, which actually makes it funny. Dooku/Gunray want to kill Padme because she'll create the army. I'm sick of weepy Padme, and this gives her personality and makes it believable that she could be Leia's mom.
