I don't think I'd change the main story much. The biggest thing I would do is try to make Anakin's story parallel Luke's a little more. Start him off close to the same age, or at the earliest maybe 16 or 17. I'd have the Clone Wars start either in the first film or at the latest, the beginning of Episode 2. The Clone wars should have been a much bigger part of the story and not just some minor inconvenience occurring elsewhere in the galaxy. I'd keep the separatists as the instigators but somewhere along the line I would have the Jedi realize that the Republic really has gone bad and that the separatists where actually right. When they attempt to stop the fighting Palpatine turns the republic against them. The separatists eventually lead to the rebellion and many of the separatists we will see will be races we saw in the original trilogy (Mon Calamari, Sullustans, ect). The whole rule of 2 crap with the Sith, out the window, Palpatine has a secret order of the Sith just like they are discribed in the early drafts of the original movie, minus the whole Kaiburr crystal thing. Would probably keep the likes of Dooku, Maul, and Asajj Ventress. Anakin will actually fall to the dark side in Episode II to better reflect the darker ending of Empire. That way, Episode III can all be about Obi-Wan being a hero and trying to redeem Anakin much like Luke does in Jedi only he fails.