Call of Juarez: Bound in Blood is most likely my favorite FPS ever, but nobody seems to remember the game exists.
Mark of the Ninja is OH SO GOOD, and it got over 90 on Metacritic but... I don't know, it seems fairly ignored.
And I'm tempted to say FFXIII, but that's a weird case. It got 80+ on Metacritic but despite that, every single critic started to bash on the game, apparently after they noticed that the internet was bashing it. I mean, wtf?
Just on a sidenote, I played Folklore. It has the distinction of having the best use for the Sixaxis, but... the game is extremely repetitive. You have two characters, but their journeys are (pretty much) exactly the same. Story is promising but confusing too. To this day, I regret buying Folklore instead of Eternal Sonata at the time. But I'd like to see a sequel, with its flaws fixed. It has the potential to be an AMAZING game - and it is, at times.