I enjoyed the first half of the game that had the tear hunts, because it broke up the play a bit, though having said that, if they'd have continued them to the end of the game i would have been sick to death of them - so i think they stopped at the right time.
The problem was they didn't replace it within anything interesting. Most of the land discovery is out of the way by that point and so finding the next dungeon was a matter of talking to the right couple of people in a row and that was it, do the dungeon and repeat.
So i thought the build up was great in the first half, but then it just lost it's pace. I was half expecting a new land or something that wasn't obviously waiting on the map to be uncovered, but it never happened.
The map is of course huge and realistic, which isn't a problem in itself, but you get the impression that it was only huge because people begged for huge. As a result, they didn't really consider the repercussion's of having a realistic map as much as they should have. There's not enough people, there's not enough towns and there's not enough interesting stuff going on other than everyone waiting around to see if the girl gets her memory back.
Most Zelda's also have this problem where as the game goes on, you become so strong and so familiar with the way the levels are going to work (you can predict stuff), that the difficulty curve is shot, and later levels don't pose as much threat as earlier ones (in terms of puzzle difficulty as well as enemy difficulty) - and you get the feeling that you're just going through the motions.
Are any of the dungeons really ordered in an accurate difficulty curve? Even OOT's dungeons had this problem, the Desert Collossus was a room by room piece of cake compared to Forest or Water. That brings me to thinking that they should adopt the 'any dungeon any order' idea, but they'll never do it, cause they can't control the flow of the game or have a detailed cohesive story without having a (somewhat hidden) linear progression. So they need to make the later dungeons harder - this was best done in LTTP IMO.
Here's a probably stupid idea - maybe at the beginning of the game link should walk into a cave (yes, that cave) with every fucking item, and as he goes through the game he becomes cursed or something and gradually loses items. The difficulty would increase and they could come up with some puzzles that relied on preconceived ideas of 'i need that weapon' - but you don't have it, so figure it out a different way. Of course, it's no fun having no items
Finally, Midna and her story was great, but seemingly at the expense of Zelda's significance in the story - who was virtually not needed at all. By the end i got the feeling that it didn't even have to be called a Zelda game.
All that said, anyone who thinks it's not better than TWW is just plain wrong. I still can't believe Jabun just hands over that third pearl, or how, for the sake of having some fancy music playing on the C-stick, you have to interrupt the already slow as ocean just to turn around. Maybe if they'd have spent another year on TWW it would have been up there with the best.