Who were you confused about?
You were trying to save the galaxy, because it needed saving and you had the means.
Kreia was, well... we know what she was doing all along. Or at least I think I do. Ask me if that's your question.
Also, this IS an RPG - if you want to know what happens beyond the main plotline, as far as your NPC's motives, you have to figure it out for yourself. If that's at all part of what you're talking about. I thought this game did a pretty good job of explaining that, though...
I, personally, am left with a feeling of, "What next?", not, "What the heck just happened?" Were you confused about who the true antagonist was? That's easy enough to clear up...