Twinmold, from Majora's Mask, as much as I like turning into a giant. It's still my favorite temple from all the 3D zelda games, but the boss prevents it from being absolutely perfect.
Plasm Wraith from Pikmin 3. Don't get me wrong, I freakin' love this thing, it's super cool. But It just doesn't fit in with the other bosses. Every other boss is based off a real life creature, such as the Armored Mawdad being a centipede or the Scornet Maestro being a bee queen, The Plasm Wraith is just kinda... There.