Annoying protagonists. That alone can ruin a game for me.
Think Lloyd, from Tales of Symphonia. I hate his voice, his outfit, his personality, his hair, his voice, his face, his fighting style, his backstory, his constant confusion, his MOTHERFUCKING VOICE, and pretty much everything else about him. I understand it if he's got his fans, but I'm just not one of them.
I know that's a bit harsh, but he has always annoyed me. And don't get me wrong; I like Tales of Symphonia. I just can't stand the characters. All of them were either cliched, annoying or just kind of stereotypical:
The clumsy one, the dark/quiet one, the nerdy one, the little kid etc. I did like Presea and Regal, mainly because they both had good backstories that were well-presented and honest, and didn't seemed rushed.
That's basically it; a cliched, overdone story with equally cliched characters can quickly become an annoyance for me. I think it's mainly because I've seen it before several times.
I know it's a universal topic, but it bothers me most in RPGs.
However, I can forgive this if the game is fun to play and actually makes the cliched characters kind of likeable. I think Lost Odyssey did this well, because it was incredibly well-done and even very emotional at times.
Also, if the game really has a unique style to it (in terms of graphics, landscapes and universe etc), that's a huge step upward for me. One example is Baten Kaitos which managed to create a beautiful world and likeable characters that I ended up caring for, as well as wanted to see more of.
Aside from this, I'm not really sure. As long as the game is understandable in terms of combat, it's not a big problem for me.
I know this mainly concerns JRPGs, and I apologize if the thread wasn't really aimed at that. It was just the first think that popped into my mind.