How's this for radical?
Make the jedi council and the republic the villains.
Make the Seperatists/Dooku the good guys.
The federation would be the beginnings of the seperatists, replacing sidious with dooku and replacing the dialogue it is set up that they attack naboo (changed to alderaan) in a political gambit, a desperate attempt to defy the fascistic leaders of the republic.
Qui-Gon Gin's actions in the movies have always been arrogant and counter-productive. We could explain this by making him an egotistical typ of character.
Think about this: The Sith have been extinct. They were hiding of course we know that, but there aren't many. The council believed them to be extinct. So the jedi are the only force users for hundreds if not thousands of years. And then there's a prophecy to bring balance to the force. And they think that would be in their favor!
It's all a perfect set up to switch the roles around, I would say.
Count Dooku's death in the third movie would have meaning to it, the story would be more emotional as the seperatists lost more and more, resulting in an utter defeat and complete ruination of the republic.
It's like with the rebels in the ot, but it goes the other way.