Zelda II: When the game was brand new, I don't remember many kids hating it. But when I was a little older in the 90s I knew plenty of kids who hated it, and this hate definitely pre-dated the ubiquity of the Internet.
SMB2: This game was always super popular until it was revealed that it wasn't the "real" Super Mario 2, and then gradually it got more Internet hate later on because of this. Ironically, I see virtually no one say how great a game the REAL Super Mario 2 / Lost Levels is.
Doom on SNES: Is this a thing???? I thought the earliest Nintendo console doom game was Doom 64.
Majora's Mask: I HATE that game, yes, because of the 3-day thing. I didn't know it was roundly hated though. I never saw a whole lot of discussion about it, and what little I did see was mostly positive.
Wind Waker: Everyone and their mother hated the game BEFORE IT WAS EVEN RELEASED solely because of the graphics. But I thought once it was actually released and people actually played it the public decided it was actually a good game after all. I stopped playing new games by the time of its release, so I've never played it.