Ok here is my 2 cents.
I think that you should start out as a force-sensitive who has been called to the Jedi Temple on Coruscant. You should start out on your homeplanet (Alderaan would be cool), and along the way you would meet some sith who are trying to kill anybody training as a jedi. You fight through them, and end up having to find a small shuttle with... T3! Apparently you can't find out much from him and he won't tell you much about what he does know, but he follows you to the jedi temple. You begin training, and i mean actually training, like maybe going to different masters to build your lightsaber, learn a saber form, and actually spar with other padawans, stuff like that. You could even take a test or something to get to the next level of training that required you to give information(gender, face, alignment) about Revan and Exile. After you have maybe gone on a few missions, you have a vision of Revan and the Exile, and it seems that a select few other notable padawans had similar visions. You are sent by the Jedi Council to either Kashyyyk, Tatooine, Manaan, and Korriban, (take your pick). You are sent with a female padawan who will be the main female character in your party, and maybe if you wanted to go to more than one planet out of those 4 they could make something happen to the Jedi that went to your second planet pick and you would have to go there also. Eventually the three or four Jedi meet up on the unknown world and there your training would end and you would be on your own.
Next you would learn more about the Exile by looking at some of the planets he went to. After this you would head to the Malachor V system and head off into the unkown regions (you would probably pick up a few characters from all of these planets). You would find the Ebon Hawk, little more than a floated hulk in space. After repairing it it becomes your ship and you follow the last set of coordinates it was at. AT this point, I don't have a set idea on what the storyline will be, but i think that you should head around to uncharted planets, some with big cities and architecture yet mysteriously empty, some seemingly uninhabited planets with forest or grasslands, and some places with sith lords and there minions. All of these would have subtle clues leading up to the last planets. It would be cool if you were also hounded by the Genorharadon (elite bounter hunter society in KOTOR 1). Eventually you find Exile and Revan, and at the end have a titannic battle between Jedi and Sith (maybe the "true Sith).
OH MAN! Finally thats done with.