I would like to second (and third, etc) the opinions that the third would have to resolve the storylines of Revan (and hopefully the Exile). I haven't given any thought to the complexities of the storyline however, but I do think it should provide a form of of external 'browser' that imports some save game data from the previous titles (or makes generalised assumptions... as distateful as that may sound) to weave the tale for the third.
I don't really think that in the third game, NPC's of Revan or the Exile (or even PC's) are actually warranted. What is needed is closure of some sort yes, and while it would be benefical to have them in the 'flesh' as it were, it isn't really needed. Perhaps a datapad or something that leads onto their fate. This is admittedly a very ugly solution, but I think it still manages to create closure (whatever that may entail).
Furthermore, I don't think actually allowing the third game to follow their footsteps per say is a good thing either, for the simple fact that if you do meet and fight 'the true sith' you would destroy episodes 1-6 ("Hi, I work for the republic!" "What republic? They were destroyed by those alien overlords about 4000 years ago. I think you should of stayed under your rock"). Afterall, it has been said, repeatedly I do believe, that True Sith are a lot more adept with the dark side than mere mortals. In that regard, I think it's next to impossible to have a 'happy ending' with Revan returning to Bastilla (OMG... she is so 'hot') or Carth, or the Exile returning to Visas/Handmaiden (I prefered Mira, although I don't think that option exists).
I know that KOTOR doesn't stand for 'Knitting ... Tales Of Revan,' but I think the majority of the success of the second one is because it dealt in no small part to Revan. After-all the 'pimping' of Revan in the first one (the greatest military strategist'), and that revelation, it would be criminal of Obsidian to ignore it I think. Like it or not, Revan is a central character to the tale of Knights of the Old Republic. It would be like removing Luke Skywalker after New Hope and Empire Strikes Back, and replacing it with Rex - The Uber Mastiff or something. It would of absolutely destroy the movies' success, and I think if Obsidian (or someone else, anybody else) did it to KOTOR then it would be the same mistake. Personally, I have become more attracted to the characters of Revan and the Exile (and to their supporting cast... except T3), and to re-iterate, I think it would be poor form and would loose a significant portion of potential customers if they did remove them.
Yes, any story they develop to continue the story is going to be fraut with massive difficulties, and I don't really have a solution to it (I really don't envy the poor sod who does have to do so), but I think the conversation pieces in TSL performed adequately for the task, and I suppose you could just 'mirror' the Exile's fate with Revan's (ie, he received some sort of 'force prompt' to help Revan (or to slay him to consolidate his own power) that would let them embark into the 'outer regions' to pursue Revan.