I felt the biggest weakness was the second half didn't seem to flow together at all. It was all these great dungeons, but they felt like a half dozen independent design teams had made them and put them all in the same game. And I mean, I know that happens in Zelda but it just didn't feel... polished for me.
The first half of the game, while slow at times, felt like they had worked to tie stuff together. Characters make sense, you have a distinct reason to do things, it was all building up.
Then the end just unraveled. The story stuff is tossed aside and you are just left with dungeon hopping with nothing else. And yeah, they're great dungeons individually, but they don't make for a great second half of a game.
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http://img.imgcake.com/nio/51alecpngpa.png -Nio