I have to say Darkspore is the first thing that comes to my mind. I doubt anyone's heard about it. It gets like, mixed reviews and a 6/10. Sure, it's a hack and slash game with RPG elements, similar to Diablo, but it controls nicely and does its job of being satisfying to kill enemies. It's a bit repetitive at points, and it DOES have the stupid always on DRM crap, but it stands out for its Spore-like editor which takes customizing your character to the max.
I also think Super Mario Bros. 2 USA gets too much hate for essentially being a reskinned Doki Doki Panic (when that's not necessarily true) and it constantly gets overlooked by Super Mario Bros. 3 and Super Mario World. I had more fun with Super Mario Bros. 2 than those two games and I think it should get more love.
Another contender is Mario Kart Super Circuit. I think it does deserve the good reviews it got and its GameRankings and Metacritic average. I think the main reason it gets criticized is that it is compared to more modern games, because the handling in Mario Kart Super Circuit is very similar to Mario Kart 64 and Super Mario Kart. It also has very creative, memorable tracks (and the most race tracks in the series so far) and I think it does a good job at being the first handheld Mario Kart. It's overshadowed by more modern games, but it shouldn't be forgotten.
I would say the Mario Kart Arcade GP games too, but they're more overshadowed than hated, really.
Mario Party games should get a spot here. I constantly see criticism for being the same game over and over, but I still have fun with the game. I don't think it NEEDS any major core changes; just look how botched up Mario Party 9 and Mario Party: Island Tour are. I think the Mario Party games are fine as they are: they need some few changes to shake things up a bit, similar to Mario Kart. The game is meant to be played with friends, so I still don't understand some of its criticisms of how repetitive it can get or how boring it is. The only one I CAN get behind is lack of online play. Seriously, it's a multiplayer focused game, it'll DEFINITELY benefit from online play, which should be a staple in ANY multiplayer game these days.
I'm going to mention Spore too. Though its core game is a bit lacking, the creature creator is simply the best customization I have ever seen. It's truly amazing. What makes this game even better is its expansion pack, Galactic Adventures. I think THAT should be the core game instead of what we have. You can basically do virtually ANYTHING with Spore Galactic Adventures. You can create a Mario Kart adventure, complete with checkpoints and objectives, you can just do random crap like blowing up enemies and killing them without any sort of objectives. The scope of creation is limitless and it's easy to use and fun too. With the creator creator, vehicle editor, and building construction, and the vast customizable terrain, I'd say it's one of the best games for creativity out there. I can get behind that Spore can be considered a shell of its former self but its expansion pack kinda does it justice. It's a shame EA had to abandon this...