Worst parts of otherwise great games?

The Forsaken Fortress stealth mission at the beginning of Wind Waker. It's what stops me from replays since it's right there at the beginning. The Triforce Hunt is pretty bad too but not as bad as I thought it would be when I last replayed the game.

Bravely Default: You know why.

Some of the underground areas in Pikmin 2 are obnoxious, especially the ones found in the final area. Oh, and of course, Submerged Castle.

Any swamp area in the Souls games, but they're kind of iconic at this point.