Heh, for me, the Revan twist was the one that was spoiled for me (in this case, by a friend who didn't realize that I didn't know yet). I was too young to remember what I felt about the "I am your father" thing.
Well, at the beginning, you're just trying to escape Peragus and then recover your ship, and then you're looking for the Jedi Masters. But yeah, after that, it's kind of convoluted and hard to tell what's going on. Not the best think in my opinion.
One issue I had was similar to this, except that I felt that whatever I did in the first game, especially if I faithfully followed the light side and saved the galaxy, was largely irrelevant and played down. It was kind of annoying.