1. Artificial difficulty:
Controls make it hard to pull something off even after you know exactly what to do and how to do it. This is different from Genuine skill-based difficulty which would be based on timing relative to something on screen for relatively few button presses. (For example: Jumping at a precise time to make the leap successfully is genuine difficulty. Hitting 5 buttons in rapid sequence while twirling the control stick precisely 270º is not.)
Computer controlled characters pull off things that can't possibly be done by a human character.
2. Crazy abilities in-cutscene but regular joe outside cutscene. (Many games are finally fixing this. Point is, my characters should never be able to do something in a cutscene that I can't do with them outside the cutscene without adequate explanation.)
3. Pointless length: FFXII, for instance, took about 50 hours to play even though there were perhaps 10 hours of actual story. So much time was spent running from one place to a distant other that the experience felt pretty disjointed. When just playing through a story-heavy game (not doing sidequests / extras), you should not have extremely long sequences of very basic gameplay and absolutely no story development. (Not necessarily cutscenes, but at least some occasional text / dialog).
4. Random badly implemented cross-genre sequences. (Gummi ship in Kingdom Hearts, random vehicle levels in shooters, etc.)
There are more, but I can't think of them at the moment.
