Too many Riddler puzzles
You know why the Batman villain The Riddler bugged me? Because, while there was a "correct" answer to his puzzles that remotely followed some trail of clues, the clues in themselves were not self-evident to anyone (other than Batman, somehow). This game suffers from the same problem; when you know the answer already, it kind of makes sense how the clue hints at it, but most of the time the clues don't help to find the answer and I have to use both of my hints, which make me feel stupid, because the girl practically gives you the answer instead of a better clue, as if it was obvious. The riddles were (usually) pretty good, so I'd focus more on those next time. Graphics, music, etc were all great, it was just the puzzles that bugged me.
(Spoilers ahead)
Of most note was the damned cell phone puzzle. How the hell was I supposed to know not only that the answer wasn't the name of an object (as was implied by the ransom note), but also to hit each button multiple times to come up with the number?