Well, I've always thought that Dooku would work magnificently as a Jedi who believes that the only way to defeat the Sith, who are slowly overtaking the Republic, is to go on an all out war against it and take over.

Tragically misguided, lured into the Dark Side and not entirely a "hero" but rather a ruthless, dedicated leader with good intentions.

And the Separatists (who should have been formed at the beginning of Ep.I) could have been the twisted version of the Rebel Alliance.

Instead of poor but heroic rebels, the Separatists are initially rich and power hungry human and alien star system who eventually are united by the fear of an increasingly brutal Republic, and fighting for independence. Over the course of the movies you get to sympathize more with their cause, however flawed it was at the beggining.