I agree with TwiliMajora on the Sandship. There was nothing exciting about the Sandship, it wasnt epic at all, and honestly, I felt no sympathy for the ancient robots and skipper. Theyre a bunch of robots for pete's peppers, how did Nintendo expect me to care about that? Of course, you go to the Sandship to get to the flame, but still. There was nothing exciting, and oh mah gahd the mini boss was insanely easy for one of the final dungeons in SS.
I also wasn't a fan of the Wind and Earth Temples in WW. The Earth Temple wasn't insanely boring, it was still interesting, but I just didnt enjoy playing through it. And the Wind Temple. Aghhhhhhhhhhhhhhh. The music pissed me off sooo much, it's like something that plays in the background while youre being tickled by an evil clown... and the Wizrobes in WW were insanely annoying, I can't elaborate enough on how much they got to me, it was like a bunch of Toucan Sams on acid.