Nice thread! Yes, I feel the same way - quitting seems wrong, but you have to weigh the time you could be spending playing a fun game.
Some of the games I quit:
KH-DDD: Agree with you fully, the story was just nonsensical if you haven't played the previous KH, the combat was repetitive and that annoying combat music just started to get on my nerves.
BioShock: Found the idea of Rapture just too unbelievable - can't immerse myself if I'm not sold on the premise. The FPS mechanics were also quite poor - the gun was held to high, obscuring too much of the visuals (I played on PC in 4:3 aspect ratio, maybe this problem was better in 16:9 but I doubt that it could save the game for me).
NFS Hot Pursuit on Wii: I think the performance of the Wii made some of the time-controlled missions simply impossible, or at least very very difficult. Still, it was a fun game, and since I rented it, did not mind not finishing it in the end.
Zelda OOT 3DS: Although I enjoyed the game, I encountered a bug that prevented me from continuing about 10 hours in. No way I'm replaying 10 hours - it was fun but not THAT much fun.
Batman Arkham City (Wii U): I think the game is good, but I simply do not enjoy the Batmas universe. Same thing as BioShock I suppose. I also played it at a time when there was a lot of other stuff going on - it just sort of fizzled out for me. I think I'm about halfway in the game, but can't find the motivation to continue now.
Honourable mention:
MGS Snake Eater 3DS: I AMOST gave up on the game during the boss-fight with The End. It just seemed impossible - I tried it for like 20 times and never even saw the guy before being taken out. Then I left it for a few weeks, and came back - and found that by pure luck I stumbled upom him ZZZZ-ing away, and could get enough shots in to end it. It would have been a pity if I gave up, because the rest of the game was really really awesome.
