I hated the idea of the "Sith," especially the way they operate in the current PT.

Maybe we can twist the thing a bit. What about the Sith (don't even mention that name anyway) being "separatists" Jedi?

I can even see the movie starting with a reunion between a Queen, a Trade federation and two arriving Jedi, unless the Jedi actulaty kill everyone.

This create a tension between the republic and the Jedi council. Yoda is under arrest for being the leader of the Jedi, and Obi-Wan leads an inquiry to redeem the honnor of his master.

I don't know where this story could go though, just an idea.