Higher Game: I actually liked KOTOR2, a lot. I agree with you that the story was a lot more cerebral than in KOTOR, and it raises some ideas that are at the very least interesting, whether you agree with them or not.
I think you've missed the point with Kreia. She's not a proper Sith any more. The Sith still believe in evil and selfishness and "might makes right", not unlike Ayn Rand; Kreia went through some soul-searching after she was cast down as Sith Lord, and now she's got this weird philosophy of not-good but not-evil and not-neutral either, which makes her an annoying old bat, but at least she's an interesting character with a personality. I liked that bit.
The problem with the ending is that a story needs to build up to a climax: Emotions come to a head, plot threads are tied up, questions are answered, and the audience gets a resolution to everything that went before. Then an epilogue to let you settle back, and then the end. KOTOR1 had a very simple ending, but it did all this. Planescape: Torment had a brilliant climax and a beautiful, bittersweet epilogue.
KOTOR2 ends like a shaggy-dog story, and unlike those, it isn't even funny. In the final confrontation, Kreia answers all your questions as if she's bored with the whole proceedings:
"What now?"
"You expected some great big revelations? Nah. We just fight and that's it."
"What about Revan?"
"Gah, she's out there, somewhere. Who cares?"
"What about my friends?"
"Ah, they'll live on until they die of one thing or another, as people do. You know, the usual."
"What about the galaxy?"
"Oh, it will get on with things, like always. Doesn't matter."
"Yeah, well, all right, but what was it all about then, this whole adventure?"
"Tcha, nothing in particular."
If this were sex, you've just had some nice foreplay, followed by an "excuse me, I have to go take a piss", and then going to sleep without a cuddle or a cigarette or anything.
It's no good saying that it's a "cliffhanger ending" as in Empire Strikes Back. Yes, the empire is winning, and Han is frozen, and everything's gone bags, but it ends with at least one big revelation: "Luke, I am your father" "Noooooo! It's not trueeee!" "Yes it is. Here, I'll cut off your hand. Let's rule the galaxy together." "Aaaaargh! I'm falling to my deaaaath!" "Luke! We've got you! Now let's go rescue Han!" The End.
See, that would be a climax, there.