Psi-Ops: The Mindgate Conspiracy was a pretty bad third-person shooter with an absolutely incomprehensible story, but the psychic powers were hilariously fun to use, at least, when the game was giving you free reign to tear stuff up. Also had some fun boss fights. I still consider the one against the big black guy with TK powers one of the best boss fights in recent memory.
Red Dead Revolver was a forgettable third-person shooter with annoying controls, but it had a good atmosphere, some nifty gameplay mechanics, good music, and a brilliant sequel >__>
I honestly don't think Alpha Protocol was that bad, but the dialogue system and highly interactive story turned what would otherwise be an slightly above average game into a great one.
Spider-Man for the PS1 had terrible controls, a clunky camera, boring combat, and badly designed levels. However, it also had great voice acting, tons of awesome comic references, and really captured the feel of the Spider-Man comics in game form.
Marvel vs. Capcom 1 was horribly, horribly imbalanced and generally un-fun to play against anyone who knew what they were doing. However, it had some cool level backgrounds and the entire idea was very cool for the time. Plus, again, good sequels (which sadly ditched the character specific background art
