Limiting my list to just games that actually generate controversy (as opposed to, say, Advance Wars or Castlevania, which are rarely accepted as anything other than awesome):
Pokemon RPGs (any, including Colosseum and XD but excluding Mysterious Dungeon) - Sometimes they get lambasted for being too simplistic. I say the people who think so have only tried the toned-down main single-player quest, and never battled in the optional post-game areas or, better yet, against other players. The deepest and overall best RPG series I've ever played, by far.
Super Smash Bros. Melee - See Pokemon, except drop the part about optional post-game areas and replace "RPG series" with "fighting game."
Bomberman 64 - Circular area explosions were the way to go for the series, yet the combination of fan backlash and professional criticism killed them before they even got off the ground for a sequel.
F-Zero GX - Some people want their racing games more complex. I don't care about complexity if it's this playable and this awesome in every way--music, number of tracks, graphics, sense of speed, unlockables for replayability, etc.
Dead or Alive series - Like the F-Zero GX of fighting games, but to a lesser degree since the music and levels and overall polish aren't as noteworthy. Other companies seriously need to take a hint and feature as many unlockable outfits as the DOA games, though.
Meteos - See F-Zero GX, sub in "puzzle" and other appropriate terms where necessary.
Tales of Symphonia - I don't get why people didn't like the storyline, or at the very least not the character-based aspects of the storyline. And there's also the awesome battle system and music, which help to make this IMO the best RPG since (but not better than)...
Star Ocean 2 - I'll never understand how people could love Valkyrie Profile, but not SO2. VP played like a DDR of RPGs, a rhythm-based experience with addictiveness but relatively little depth. SO2 had the same addictiveness, but added depth: fighters actually had more than one special attack, you had more direct control in battle, there was real character interaction outside of one throwaway 15-30 minute scene that ends up being all that any one VP character (other than Lucian or whatever his name was) gets for the entire game, and, as a result, the storyline was more complex as well. On top of all that, the music was superior--and, even if not superior in the opinions of some, at least more varied in genres--and the game could actually be played a second time through since you wouldn't have to sit through boring, lengthy, unskippable cutscenes. What did VP do better? Graphics and voice acting and that's it. I guess superficial aspects like that mean a lot to others.
Legend of Zelda: The Wind Waker - Catches some flack at times for the sailing or the cel-shading, but those were among the best parts; the artwork was beautiful (even if the body proportions were hideous), and if you're going to make a huge-yet-empty area for exploration, the ocean was a far better way to do it than the boring Hyrule Field of OoT. WW wasn't the best Zelda game--I actually think it's the fourth worst--but it gets bashed in areas where it really shouldn't.
WWF No Mercy - Some think that either the Smackdown or Day of Reckoning series has surpassed this by now. I say they're kidding themselves and that a game that's over half a decade old still has some features that the new stuff has yet to implement.
Final Fantasy 6 - Gets bashed occasionally for a non-linear second half that "lacks" in the storyline department. It doesn't lack at all; it just shifts focus from story to character, which absolutely needed to be done.
Legend of Zelda: A Link to the Past - Still the best Zelda.
