While Link's Awakening is definitely underrated, I also don't really ever see it get bashed. Phantom Hourglass, however, gets a ton of hate I don't think it deserves. The touch controls were solid and responsive (aside from rolling), the story wasn't worse than anything else in the series, and Linebeck was just amazing in general. That archery game can bite me, though.

Then Spirit Tracks (a fine game, too) gets praise over PH when I found it much more frustrating in comparison.