Same idea as the "Games that don't deserve their soundtracks" thread. It really irks me to see games in which the art department really put a lot of work and/or care into, only to end up with those in charge of the gameplay mucking their jobs up and ensuring most of those designs are unfairly associated with unfavorable experiences.
My top picks:
JSRF
Enclave
Magna Carta
Kingdom Hearts
Suikoden III
Unlimited Saga
Maken X
DOAXBV
Primal
