The archaic AI in Dark Souls. That game is just about perfect, but the AI is moronic and it can ruin the immersion. Well that and the framerate. If Dark Souls 2 fixes those two things while maintaining the excellent atmosphere and level design of the first, it could end up being one of the best games ever made.

Pretty good list^^

The difficulty of the Water Temple is extremely exaggerated, there is exactly one key that is hard to find ( If you are in the centre of the Temple, in the Tower, you have to climb upwards and play the Ocarina to raise the water to get  the door that leads you out BUT instead of leaving, you have to jump in the water again, put the iron boots on and get a key down there ...in OoT 3D the camera shows you that you opened a new way)

I hate Draygon in Super Metroid. It's a very repetitive boss and there is no point to fight it the normal way if you have the Grapple Beam.

getting information in persona 4

Oh yeah the Phazon Mines are also a bitch.

Skies of Arcadia Legends

In the first half of the game, there's a part where Vyse temporarily gets separated from Aika and Fina. Unfortunately, he ends up getting all of the money and items you've collected up until that point. As a result, his parts of Daccat's Isle (the next dungeon) are far easier than those of the girls.

The fetch quest you have to do for the pineapple mafia in Paper Mario and the Thousand Year Door. It was the one part of the game that just felt tacked on and lazy.

Ooh, don't remember me...it destroyed the flow of the game so hard...

But those Pistons the size of cities.