Came looking for this. I can understand where the hate comes from but they were so much good stuff in these games too.

gothic 3
risen series
order 1886

Skyward Sword probably.
No wait Star Fox Adventures!

Skyward Sword

Definitely agree on Spirit Tracks.

Though I didn't really care for Phantom Hourglass, Spirit Tracks is actually a very strong game, and one of the best on the DS in general. In Zelda terms, it has good dungeons, clever items and ditto use, I like the overworld that actually does have plenty of secrets to find and it has a good 'Zelda-story' where the train-mechanic has been integrated in a satisfactory way. In fact, before the WiiU HD remaster, I liked Spirit Tracks better than Wind Waker, but WWHD fixes enough to put it slightly ahead now.

Other than that, I'm not sure. Do the first two Call of Duties count? Guess not, the series is hated a bit, but I think those first two are universally liked. I thought they were two of the best FPS's ever made.

Otherwise maybe Total War: Rome II. People cried about it being 'unplayable'. While I can agree that the game probably could have benefitted from an extra month or two in the oven, I found it to be very playable and it brought some interesting new ideas to the series.

The Legend of Zelda II: The Adventure of Link. In fact, it's actually my favorite Zelda title

On PC, it's probably Supreme Ruler: 2020 and Elemental: War on Magic. Both got destroyed by critics and many gamers because of their tediousness (and bugs in the second's case. Seriously, they released 7 updates for that one in just the first 3 days!), but I really like them

Metroid Other M
Skyward Sword
Sengoku Basara
Guardians of Middle-earth
Lord of the Rings: War in the North

BMX XXX
Too Human

Super Mario Sunshine

best mario evah

Hrm. Problem here is, I imagine every game has its loyal fanbase. Here's my list of shame, I guess.

Amagon (NES), Cyborg Justice (Genesis), Paladin's Quest (SNES), Jade Cocoon (PS1), The Bouncer (PS2), Bionic Commando (PS3), Saints Row 4, The Order 1886.