EverQuest and World of Warcraft, for requiring the players to raid to see any worthwhile storyline content. I love those games/gameworlds to death, but I'll never be a raider. I just don't enjoy the hectic chaos that is raiding.
Breath of Fire 3 - The master system is really tedious... you need to read a strategy guide to really understand it, and I don't like studying strat guides so..
Breath of Fire 4 - the new dragon forms looks like crap. Dragons should NOT look like insects.
Morrowind - the game freezes too much.
Oblivion - the game freezes too much.
Fallout 3 - the game freezes too much.
New Vegas - the game is an unplayable glitchy mess that encourages you to ignore that VATS exists. Because the Fallout engine was so good at real time shooting to begin with..
Bioshock1&2 - the combat never feels 'right' in these games, enemies are more annoying than fun to kill, and the constantly immersion breaking radio broadcasts are extremely annoying.
Systemshock 2 - respawning enemies. otherwise, a perfect game.
Starcraft: the map editor was too basic and was very glitchy, triggers would often NOT perform what they were supposed to, timed events would not register at the right timing, etc.
Final Fantasy 3 - only available on the nintendo DS, otherwise a great game
Pokemon Red/Blue - see above, replace ds with previous handheld version
Ugh. I like too many games. Sorry if I broke the rules OP, its just torture to ask me to pick just one game. I could have made this list go on forever.
Edit: Oh :O it had to be done, but for me:
Deadspace 1 & 2 perfect games with no flaws (for me)
