Features that annoy me:
1: Not being able to make my own character. I want to be able to choose my own class, skills, gender, and what not. I want the character to be mine, not the designers.
2: Full Vioice Overs. I hate them.
3: Being dictated how my character should react. Baldur's Gate 2, for eample, forces you to either care enough about Imoen to go after her or you care enough about revenge to go after Irenicus. For a neutral evil halfling thief both seemed trivial and I would have thought to go my merry way, but no I just couldn't play my character. Or to even care about leaving Taris in KotOR 1, or going after Master Li in Jade Empire.
4: AI Control of party members. It is stupid because the AI is stupid. Also the party control system of KotOR 1 and 2 is the worst period.
5: Not being able have my character have the same conclusions as the player. In KotOR 1 due to the who revelation thingie I figured the whole plot twist way before then. The first time through I was playing a fairly Intelligent scoundrel/consuler type (16 Int/14 Wis, which would exceed what I would give myself in DnD stats) I should have been able to say "So what. I already figured that out." But no, Bioware had to script the character as a moron even if his/her statistics say otherwise.
6: Scripted battles. My characters could have easily taken out Malak on the Leviathon, but no Bioware lacks the foresight to notice that they made the freaking game way too easy to begin with and wouldn't lket my character kill the bugger right there and then. Clue to developers, if you don't want me to defeat your main villain do two things: A. Don't let me face him til you want him dead or B. Make him impossible to beat at which time I first encounter him. NOT BLOODY DIFFICULT!