It's 1am and I just turned off Knights of the Old Republic. While it's shaping up to be a pretty good CRPG (and, the prequel movies aside, I'm a sucker for all things Star Wars), here's the things I have found annoying so far:

1. I decided to go with the "Scoundrel" character class. Because it just sounded cooler than the other two. True to form, I later discover this is the Class You Should Not Play. I do this with every single game I play. Ho hum, I'm too stubborn to change now.
2. Sure, it's cool that you're using the d20 rules, but it'd be nice if the computer insulated me from them a little more.
3. You can wander around a populated city waving a sword without any reaction from guards or NPCs.
4. Not only are there no repercussions for looting random apartments, it's practically encouraged. You can gain a mountain of "good side of The Force" points for refusing a reward for helping someone, and then you can turn around and rob them, with no "Dark Side" points, while the victim watches and does nothing.
5. Combat is frighteningly simplistic. It reflects the tabletop roleplaying combat experience just that little bit too accurately: where people just take it in turns to roll the dice to see if they hit or not. The more sophisticated the graphics for CRPGs become, the more stupid this system starts to look as characters that should by all rights be diving for cover or hiding around corners end up standing up in plain sight, guns blazing.
6. On a related note, given I deliberately chose a stealthy character over a strong one: when I sneak up behind J. Random Grunt Guard completely unnoticed and hit him with a sword, I damn well expect him to die. I mean, I could do that with a piece of string in Hitman. Having my victim lose about 10% of his hit points and then turn around and kill me really breaks the old suspension of disbelief.
7. I have a sneaking suspicion that the plot, script and acting in the game will turn out to be better than those in the next Star Wars movie.