See, I'm one of the people that really despised the story in KOTOR 2. Not the overall plot, necessarily; that was fairly interesting. My problem was that it was really poorly told, and not just because of being unfinished. It's never clearly explained why you're doing what you're doing. Sure you find out that someone's pulling the strings, but there seems to be very little reason behind anything you do leading up to that.
Why am I looking for Jedi? Oh, for revenge or answers. That's a pretty limited scope for roleplaying, and it doesn't gel well with the character up to that point. (s)He's just spent the past few years traveling alone, now all of a sudden they want to go to random places looking for Jedi.
In general too, the game suffered from way too much angst. I always get bored when games try to be "dark" and emo. It just feels like the devs never got out of the angsty teen years.
The characters were also, mostly, boring. I hated Visas, because she was so... whiny? IDK, she just seemed too much like some goth kid's wet dream. The only interesting character IMO was Bao Dur, because he really had depth, and it all fit. Atton was inconsistent (am I a depressed assassin, or a Han Solo stand-in mixed with comedy relief?).
There was also a general balance issue. If you put any effort into maximizing your character, the last level was a joke (walk in, cast stasis field, cast Adv throw, exit room, repeat). Then, the final boss resists most force powers, almost always hits you and does a ton of damage. It was never interesting or fun fighting her, it was just frustrating and tedious.
That being said, I did enjoy the game. It's the same story with all Obsidian games: they're guilty pleasures. There are a ton of things that bother me, but I can't deny that I enjoy it most of the time. I just generally feel that their games lack polish and never really live up to potential.