I've probably said this before on this site, but the Forsaken Fortress in The Legend of Zelda: The Wind Waker.
Seriously, they give you your sword, let you mess around with it for like five minutes, and then make you go through the dungeon without using the thing (a primary game mechanic) that you just learned about. Instead, they have you going through a long, tedious stealth section. This part of the game feels so much longer than it probably is, but two things make it nearly unacceptable:
1.) This is the beginning of the game. I am actually not opposed to the idea of reducing the player's power if it adds something to the game. I just think that if you're going to do that, make the player care about the powers (or allies) he lost. Paper Mario: Thousand-Year Door does this pretty well. One chapter of the game has a Duplighost stealing Mario's body and name, and his allies have fallen for the trick, so Mario is left at reduced power without his backup. The player gets a sense of urgency for getting his friends and body back, especially since he can't continue his mission of gathering the Crystal Stars without them. Mario's shadowy state also allows him to recruit Vivian, a fiery phantom that up until now has been trying to stop Mario with her sisters, and show her that he's actually a nice guy. But what's also important is that this is the FOURTH Chapter of the game (out of eight), so by this time, the player should be familiar with how helpful Goombella, Koops, Flurrie, and Yoshi have been to him, and how important it is that he unmasks the Duplighost. Would it be such a meaningful effect if this happened to Mario when Goombella was his only companion?
2.) The stealth stuff shown in this part never happens again. You do have to revisit the Forsaken Fortress later on, but that time, you manage to go there with the Master Sword. The only thing you need to make that trip easier is to take out the cannons. Other than that, you don't have to do any of this stealth crap again. You never lose your sword again, either. So I have to question what the point of the stealth dungeon even was.
Next time I start a file on Wind Waker, I should just get the Forsaken Fortress over with, and then copy that file onto every available slot. That way, I can skip right to the good part of the game.