well before you pitch that idea and make a game based off the star wars universe you will need to be licensed to use the star wars name.
having only played minimal of both KOTOR games (maybe half way through each), i don't really have much to offer in the way of ideas (the story is kind of out of my mind now).
if you want main stream story the basic, bad sith lord causing issues for the good people of the galaxy and new comer heros destroy them, or put a spin and they could potentionally join or turn evil once they had destroyed the sith. all depends on book or game story, you could do a similar bioware game system where you have different endings and dialogue changes the story through the game, or you can have it more main stream like the jedi knight series with only good and bad direct actions.
you could also make it a more of a hack and slash game instead of the turn based standard that has been used in the last two games. something like force unleashed would probably play nice.