Well, I voted for the last option, but after reading through the thread, I've decided that a new PC with R and E as cameos would be best. They should have R and E turn full DS due to some uber-powerful Sith Lord, one who is actually the best of both the marauder and sith lord worlds. Then your character can be just an average Jedi who decides to up his training exponentially to defeat the three baddies. You could be given the option of killing them, or possibly turning Revan and the Exile back to the light, in which case they would die due to the sudden withdrawal fromt he dark taint, but not before passing they're power on to you, whether in the form of actual unique force powers or extra attribute points or a super specialized class of Jedi. That way, you could also get an extended movie where Revan and the Exiles stories are reviewed and then ended.....permanently. This would be if you chose light side, of course.
For DS, you could just rip the power from them instead of them passing their powers on or you killing them. Either way, you get their strengths, an ending to both their stories, and a new bad guy to work your butt off to off. :D
I'm also an advocate of a character generation system more like that of Galaxies, as far as appearance goes, that is. And a better dueling feat where damage is upped due to your using both hands on the hilt instead of simply one hand. I could go on, but I have school do get done. <_<