Yeah, I noticed that too when I did a quest on Nar Shaddaa, then died stupidly and tried the same thing with Kreia in the party. I sad something to her, and got influence with Atton, where I hadn't before.
I'm at the climax. So far, I have to say it's as good as the first KoTOR. It doesn't so much feel like stuff is 'missing' per se, but more like it's only AS good as the first, not better....still an incredible game, but I'll bet the devs were more ambitious than that.
I find Mira, Mandalore, and the Handmaiden fascinating. Would liked more of all three of 'em.