I know people hold it dear, but Fallout 2. Not Fallout 1, that is a great little game (emphasis on the little as it doesn't overstay its welcome for any annoyances to take root).
Now, it might be a small bias because i just almost finished a playthrough and the last section is just rough (and i don't just mean the stupid end boss fight), but throughout the entire game i had all sorts of annoyances with it (most of them due to the UI, but also stuff like followers going behind objects/walls/etc that i can't see them to check their health status and also some mechanics issues that i don't feel like starting any arguments about so i wont mention :-P). And while i last played it years ago, i also remember thinking at the time too that it was rougher than the first game.
The game is good, don't get me wrong, but i don't think it gets scrutinized as much as other games.