I think the best thing would be to finish the game first as a jedi, and then be able to choose between sith, non force-sensitive and such. The storyline would change of course, but they all play their role.
Like, for example, an intergalactic war breaks out with the joined forces of the Exchange, the remaining Mando Clans, the Czerka Corp and the Sith, against the Republic.
1ST PLAYTHROUGH:So, you make a new game and, as a jedi, you play your part in defeating the enemy, battling with sith in their temples and such, and you deliver the final blow to the enemy leader.
2ND PLAYTHROUGH:You start of as a fallen jedi who is willing to be trained by the sith. Then, you play your part in defeating the republic, and you deliver the final blow to the enemy leader.
3D PLAYTHROUGH:You start of as a bounty hunter who hasn't chosen sides yet, and you choose wether you want to fight for the Republic or the Sith, and you fight in space battles, as well as fight with the group of jedi (or sith, depends which side you chose) to deliver the final blow to the enemy leader.
CHOOSEABLE PLAYTHROUGH:Or even better, you get to choose which of the above you'd like to do...
Now, how does that sound ?