Here are some of my pet peeves about games:
1) Bioware-style two-choice alignment system: You're either Disgustingly Good or Retarded Evil. Try to be anything in between and you'll get punished.
2) Static worlds in RPG:s. Oblivion is one of the more recent examples: You can be the Savior of the entire planet, a dueling champion and leader of the most powerful factions in the world, and still nothing happens to reflect this.
3) "Moral/Significant/World Changing" choises that don't matter at all. Bioshock's little sisters are an example of this - the only reason to kill/save the sisters is to get the other ending you missed on your first playthru.
4) Games that are supposed to be difficult, but are actually just cheap.
5) In FPS games, weapon damage is proportional to their selection number: Okay, I know the crossbow is weapon number eight and the Machine Gun is weapon number four, but why does a steel bolt pack more punch than 30 HE rounds?
6) Graphics-over-gameplay mentality.
That's all I can think of at the moment.
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