Main Series:
- HM's. Dear God, I despised HM's. Terrible HM's like Whirlpool and Rock Smash, and me having no idea how to get rid of them.
- The periods when you didn't have running shoes. Not really a feature, but it got me mad regardless.
- Dark Caves that needed Flash. Flash isn't an HM, but I hated the darkened places where you needed flash to get around. Flash has to be one of the most useless moves in existence, and being forced to put it on a Pokemon really annoyed younger me.
- Caves in general. I might be in the minority with this, but I kind of hate caves in the main series (And a ton of ROM hacks/fan games as well!). Not ones like the electricity cave in BW, but just the expressionless, boring caves that look the exact same. Don't even get me started on the constant wild encounters there.
- Pacing. It was mentioned earlier, but the incredibly slow and boring start to the 4th generation alongside the 3rd generation, with really slow and boring battles... It sucks.
Fan Games:
Most of the previous stuff carries down to here as well.
- Unneeded Edginess. Specifically, the post-Reborn fangame edginess. It's really fun when you first see it, but the constant blood and guts can get really annoying and deter to the actual shock value.
- Main Series Copies. Okay, this one ranges a bit. When there are fangames that have the purpose of being very similar to the main series, I'm perfectly fine with it. However, when there are games that claim to be different but are literally the exact same, it irritates me. A lot. I always wanted to see fangames break the formula to begin with.
And speaking of which...
- Gyms. Like the generic "cool-looking building" gyms. No relationship with the gym leader at all; you just walk in there, get a badge, then walk out and the leader is never mentioned again. I'm a huge sucker for interesting and cool characters, and I end up getting so put-off by this.
- Boring rivals. Rivals with no character, rivals with a bad team, rivals with generic designs/taken from main series... Bleh. The rival should be one of the most important characters, so if they're bad, what are the other characters going to look like? Not a good first impression.
And finally, my biggest pet-peeve that I whine about the most...!
Bad characters in general. Seriously. These guys hold up the game to begin with--they derive the story with their actions and hold the gameplay with their teams. When they're squandered, it just feels like a mark of a badly made game, and it's difficult to recover from that. It doesn't matter how many features your game has, or how pretty it looks. If the characters are unintentionally bad, I'm out.