Well, they got so much right with the game :). But if I have to say one thing...the dungeons of it were the best design I've seen in a Zelda game. They feel challenging, but once you take a look and think, you can discover the solution. It's satisfying when you do. And they all have well-designed themes and looks :D
Everything about it's great: the music, story, characters, mechanics... When I beat the game I was hoping for a Hero Mode, but it's not too bad that they didn't put it in, since it's fairly long compared to other Zelda games.
And did you know the provinces contain the names of the Goddesses? Lanayru, Eldin and Faro(re)n.