Since a lot was cut to finish the game early thats why we are left with so many questions. Yet if you think about it, thats the way the Star Wars universe is. The second anything is meant to fill in the gaps between the first and third.
KOTOR1- Was what happened after the Mandalorians wars, stop Malak and the Star Forge.
KOTOR2- Where did Revan go? What state is the galaxy in now. Obviously even if you had finished KOTOR1 as a Sith, you couldn't destroy the Republic or that would cancel the actual movies and the Emperor etc. Even having most of the Jedi killed off was a stretch seeing that Vader and the Emperor did that in the future and the Jedi were at full strength then.
KOTOR3- Will have to deal with this greater threat. It was even hinted in the first game that the council saw something that made them wait to defend against the Mandalorians and like Mandalore said what would have happened if they had won rather than Revan going to defeat them, maybe the galaxy would have been better equipped to fit off the "true Sith". But since they've drugged out why the council didn't intervene that will probably come out in KOTOR3.
Now in comparsion:
Episode 4: We learn all about Luke being the new Jedi and the evil Emperor, the rebel alliance and defeat the first Death Star (in KOTOR1 StarForge).
Episode 5: ends with Han being all frozen and the Rebels losing, blah I HATED THIS MOVIE cause the bad guys look like they are going to win, yuck yuck yuck, and you find out about Vader being Lukes Dad (okay evil Kreia reference here as Revan's first Master and if you are light side she wants you to "save" her)
Episode 6: Rebels win, destroy the second Death Star, Luke becomes full Jedi and all that, and "saves" Vader.
So see Star Wars has a history of the second anything STINKING... At least the story for KOTOR2 was good, in pulled you in that is until the game started bugging and cut scenes were missing and the driod factory didn't make it. That's not really the writers fault, thats the game manufactors for not saying "No, we're not releasing early we are going to finish this game" and then still sitting on their butts for two months and not at least finishing the PC version. If they were to replace the missing parts I'm sure alot of our questions would be answered.
Hopefully they will release a completed thrid game or re-release KOTOR2 in its completed form, sort of like the re-release of Morrowind with the expansion packs.