mephistodesigns
Hate has made me powerful
that's exactly how I pictured it as well. Here's my timeline spliced with what I thought was handled well in the PT.
I figured EpI would establish Obi-wan and Anakin's (in his late teens or early 20's) relationship, show how heroic and good they both were, and start the clone wars by the end of it. During the film, he could meet and fall in love with Padme. They kind of bond. Maybe even get married in the end. They could have pretty much handled that the way they did in AOTC. Make him her body guard so they're kinda stuck together. Palpatine could get himself elected chancellor in pretty much the same fashion as EpI, because Vallorum fails to act against the Separitists, who blockade or attack Naboo. Then bust out the clones.
II would be Anakin, due to whatever was going on in the war, all the fighting or whatever, starting to get evil. He'd marry Padme (if he didn't by the end of 1). They'd show the jedi acting as generals. See the toll the war is taking on the Jedi, the sorrow they feel at losing so many Jedi for a cause they aren't even sure is right. Have the rift between Anakin and Obi-wan grow, Anakin belileves in the war, he sides with Palpatine. It gets relatively overlooked because many jedi are split on this issue. Towards the end, we would have Anakin summoned to Palpatine's office. He would explain the Sith to him. Convince an almost already willing Anakin to join him. Anakin would turn, and be sent on some mission like in ROTS. Almost at the end, Anakin would fight Obi-wan. Anakin would reveal Palpatine's identity, confident he will win, so it won't matter if he rubs it in Obi-wan's face a bit. Obi-wan would manage to win, though it would be close. Obi-wan would leave him for dead, take his lightsaber. The Jedi would mourn the loss of Anakin, both physically and spiritually. Maybe even add his bust to the lost 20. Maybe then have Obi-wan convince them not to. Show that he is still Anakin's friend. He understands Palpatine has no doubt been polluting him all these years.
Then three, like ROTS, Palpatine becomes Emperor. Destroys the Jedi in pretty much the same fashion as ROTS. Some Jedi go to confront him, suddenly there's this Darth Vader on the scene. Vader hands a bunch of council members an @$$ whooping, really show how powerful he is. Palpatine expoits it, turns the puplic against the Jedi, claiming they have joined the Speparitists, and tried to assasinate him, had it not been for his aid, Darth Vader. Vader then goes to destroy the temple with a bunch of clones, maybe comes in contact with Obi-wan, who Vader would taunt, because it would totally be in his character to want to sort of get the last word by still being "alive". Obi-wan would try to redeem him and it would fail. Obi-wan and Yoda flee with Padme who's pregnant, time it so the twins would have been concieved before The Fight, and a few senators who want to stop Palpatine (Mon Mothma, Bail, and whoever else they want to throw in there. Then the Empire would be shown hunting down the Jedi. Vader would be shown hunting them down, killing them one by one, trying to find Obi-wan most of all. Intercut would be scenes of the twins being born, plans for the future developed, Yoda would go to Dagobah, Obi-wan takes Luke to Tatooine. Bail, Padme, and the other Senators go to Alderaan. Padme lives apart from Bail, and gives him Leia. This way she can watch over her as a family friend. But she wouldn't be directly her mother. This would explain why Leia, {who maybe could find out who her mom is in a book before ANH, show Padme just sort of waste away and die in the same book} describes her as kind, yet sad. That would be my timeline.
I think he handled a lot of the overall plot pacing fine in AOTC, and ROTS looks to be well done as well. But they both seemed crammed with info where as TPM took time for a race, had a failed attempt by Palpatine/Sidious to start a war (oooo, failed attempt, we needed to see that to understand the other films) and the only overall meat in the story was finding ani, palpatine becoming chancellor, and the sith being revealed. Other than that, it had a lot of wasted time.