I am no good at this but this seems interesting
OK I am not that great at creating story lines but how about scraping the whole idea of a hero and villain and go with the current Anti-Hero trend.
How about the game is about a survivor from the reborn experiments that doesn't want anything to with either side because he doesn't trust anyone after whats been done to him.
This guy would be a true Jedi Outcast since he would have no right to have force powers in the minds of both the Sith and the Jedi.
The jedi would see him as a dangerous loose cannon that must be stopped.
The Sith would see him as their property that has gotten loose and seek to force him back to the darkside.
Anyway like I said I am no good at these things but I figure this could be cool.
PS I agree with the TIE FIGHTER thing. That game was the best star wars flight game IMHO.