Skyward Sword is up there with Wind Waker and LttP in my top tier of Zelda games, though I might change my mind if I give it a second pass just in case it turns out to be like Twilight Princess, which wowed me the first time through but was more conspicuously flawed once I returned to it. It might not be the best answer, though, because Skyward isn't really widely loathed by any means; it was praised to the heavens on release and right now it's going through the "Zelda cycle" hazing that every game does until the next one comes out. And I was never on board with any of the detractors of the motion controls.
My answer to this may actually be Bravely Default. I can understand why a lot of people are sour about where the game goes after thirty hours or so, but I found the job combinations and battle system so engrossing that none of this mattered to me, and I was only too happy to see the game leave enough breathing room for me to experiment with new strategies against the later optional bosses. The criticism of it is fair, but was so, so far from wrecking the experience for me that Bravely D remains in serious contention to be my favourite new release of 2014.
The one game that I think is genuinely despised out of all reasonable proportion is Other M, but that isn't to say I loved it; I merely enjoyed it enough to run it through to 100% without feeling like I'd wasted my time, and after that I put it away. (And I would almost tempted to say the same of Paper Mario: Sticker Star, but by the end the "inventory check" boss design in that game put me off, and I never did finish it despite getting very close. Meanwhile, Super Paper Mario is definitely underrated, but not exactly hated either.)
NES Remix has opened my eyes to the glory that is Clu Clu Land.
