Some very interesting ideas Mrbo, but do you think they'd be possible with the material there is?

Personally, I like that the Clone Wars were orchestrated by Palpatine. It's one of the better executed elements of the PT, I think. I agree with you though that a more coherent storyline over the three movies would be better, but I think a focus on Anakin's fall would be better. Why should we care about an organization we don't know that much about to start with? At least we've seen Anakin's rise (somewhat) through the movies.

My idea for the PT would be this: make the Trade Federation in TPM the first Separatists. They blockade Naboo because they want to use the planet's resources for the war they plan to wage against the Republic.

In AOTC, we learn that despite Naboo's victory over the Separatists, the movement has only grown and an arms race has taken place: the Separatists are upping their production of droids and the Republic has created a clone army. The vote Amidala returns to Coruscant for is whether or not to deploy the army on Republic worlds.

ROTS would play out pretty much the same.

A few concepts I'm thinking about (some I picked up in this thread):

Remove the virgin birth and Midichlorians, but keep the Prophecy. I think it adds a bit of mythology to the PT. The PT has no "history".

Have Jango Fett be nameless in AOTC and have him be hired by Sidious to lure the Jedi to Geonosis to start the war, to take away any confusion about what was actually Palpatine's plan, and what was coincidence.

Show Sidious' "Emperor" face in the holograms to add to the surprise that Palpatine is Sidious.

Have Bail Organa be the one to give Palpatine emergency powers. It would make his character a bit more integral to the story, but would also give him a motivation to start the Rebellion in ROTS.