I'm not sure if it counts, given that it was published by Nintendo, but Xenoblade Chronicles would easily be my favorite non-AAA game of this generation. I guess I find it hard to view it as AAA when the only advertising I saw of it was in Nintendo's newsletter and it was only sold at Gamestop. In any case, it nailed pretty much everything I'm concerned with in video games, and while it certainly had some flaws, those flaws hardly hindered the experience when held up to its many strengths.
For those who don't accept games published by large companies like Nintendo, then it would be a toss-up between Braid and Super Meat Boy. Braid, regardless of its extreme pretentiousness, is a game that I just fell in love with and I go back to play it probably more than any other game this generation. Super Meat Boy was just a really fun experience that brought me back to many of the good 2D platformers I played growing up.