May as well start by agreeing with everyone above (except on the point that the Sanship is a good dungeon. I found it really boring, personally). Tentalus starts off great, running through the ship as it gets smashed up, but then it's just a goofy children's cartoon character and quite pathetic. While we're all going over how bad Skyword Sword is again, Ghirahim is a hugely disappointing boss fight. I can give him a pass for the Skyview Temple (just barely, mechanically he's literally a bokoblin), but when he turned out to be the boss of the Fire Sanctuary I was so let down, especially as the fight wasn't significantly different. I knew I'dhave to fight him again, and his final fight is also just more of the same: Wait for him to raise an arm, attack from opposite direction, rinse, repeat. Demise is another glaring example. The pure manifestation of evil in the world and you can literally beat him by laconically waving your arm left and right, which I did on my second playthrough to prove the point. The only boss worth note in Skyward Sword is Koloktos, mainly for an interesting design (the fight is another 'look which direction to swing, execute' affair).
Christ, that game is so boring.
Outside SS, the first two bosses in Crash Bandicoot 2 are really disappointing. Ripper Roo is beaten by literally standing still in a secific spot six times. No challenge, no drama. The Komodo Bros are also pathetically easy. It's like they aren't making any effort to hurt you. The final battle with Cortex is also a major disappointment. You have a jetpack and chae him along a path. Hit him three times and he's toast. Hardly what I'd call thrilling or challenging.
Almost all of the bosses in Resident Evil 0 are disappointing, too, because many are just giant animals, like the giant scorpion on the train. Wow, so creative, Capcom. I'm really horrified by the implication of the T-Virus knowing it seems to just make things bigger. Bone chilling...