I didn't like the petty evil options in the first game (but then, I play Light Side, so it wasn't like I was going to take them anyway), but they were at least recognizable as evil.
In the second game, I got actively pissed off when dialog options that were only sarcastic earned me dark side points. I don't complain if talking about love of battle or people deserving to die gives me a dark side point, but if being snarky is enough for me to suddenly grow black veins on my face, that's just stupid.
That may be the difference between Obsidian and BioWare in a nutshell. BioWare can be clumsier, because that clumsiness is an attempt to make sure that everybody knows what's going on and what choices they're making at any given time. Obsidian's dialog can flow more naturally, and the choices are often more ambiguous morally. The good news is that that's more nuanced. The bad news is that nuanced doesn't help when you put the game down for a week and then come back to try to remember what you were supposed to be doing — and can also lead to times when the player is pissed off because the game didn't explain things to them.
As somebody who gets huffy about being slapped with Dark side points, I think I'm at the right company. That doesn't make me better. I suspect some people will quite vocally declare that it makes me worse. I don't think it's either, though. It's just a difference in playstyles, why we play and what we want. I want to be Mister Glowy Sparkly aura of awesome. That's what I paid $60 for.
(I also can't wait to see how Obsidian does with Alpha Protocol. I think it's a better IP for the type of games they produce. I enjoyed KotOR 2 despite its flaws, and I enjoyed what I played of NWN2, but I think they'll shine in an IP that doesn't have an actual hard and fast morality unless they want to make one. I hated having Darth Old Lady explain moral ambiguity to me, when I knew that she was evil the whole time, and she and I lived in a world where evil spellcasters got ugly crap on their faces to make it pretty damn clear that no, giving the guy some money was not actually a morally twisty act with consequences that I couldn't possibly understand, Darth Old Lady was just being a dink and needed to stay on the ship.)