-Parasite Eve II (this game doesn't get half the appreciation it deserves):
The unlocked extra weapons are only available in the easiest setting, which is just total ass for the obvious reasons. Some of the puzzles are also a bit hard to figure out, and the final boss battle is a pretty brutal difficulty spike, though it's also the most epic battle I've ever seen on PS1, so that balances it out a bit (well, the most epic in an action game anyways... >_> *Final Fantasy VIII*).
-Infamous:
Once you beat the game and have cleared all the areas, the game is pretty much devoid of enemies to mess around with using your awesome powers. I guess user generated missions in Infamous 2 somewhat fixed this, but I haven't bought that yet.
-Silent Hill 2:
The game showers you with ammo and medicine, so the whole survival aspect of survival-horror is missing. And why in the name of everything that is good did they not include the same unlockable camera view they had in the original Silent Hill? This goes to Silent Hill 3, too.
-Shadow of the Colossus:
Zero replay value for me. Nada. Once you know how to beat the Colossi they become total pushovers even on the Hard setting, which really kills the game for me.