On a side note: I'll actually be able to play Skyward Sword now that I'm getting a WiiU. Yeeees!
Skyward Sword to me was the weakest. I've played every "main" Legend of Zelda game since I played the first in 1990, and the subsequent when they were released. Skyward Sword, really had some repetitive stuff, in it, poorly designed world, felt too linear.
Now having said that is it a bad game? No, it's still a great game, just compared to many other Zelda games I'd say it's right above The Adventure of Link, which is my lowest. I felt they tried to do something too different with Skyward and it just never works out, same with Wind Waker. I would rank them like this.
1. Ocarina of Time
2. A Link to the Past
3. The Twilight Princess
4. The Legend of Zelda
5. Majora's Mask
6. Wind Waker
7. Skyward Sword
8. The Adventures of Link
I think they should look back to OOT and really get a feel on how to create such a wonderful world/dungeons. OOT felt so unique and still does, just great lay out, felt like a massive world. The problem with Twilight Princess was it felt way too small, mainly so they could layer two types of worlds on top of each other. But still I hope they take lessons from this.
Skyward Swords biggest problem was just it's motion control. I mean I finished the game, and liked it. But I just never felt like I did with previous Zelda games. The motion control really actually made many of the new items weak, and just never felt cool for some reason. I would fight with the motion control way too much. I think games like Mario Galaxy worked with it, but this sure did not.
I hope with the next one they take advantage with the new system and hardware, and make a very large game, something inspired by OOT. With lots to do, and fun stuff all around. The mini games in Skyward Sword were just weak.
Well enough of my rant, I hope Zelda U rocks the house.
EDIT: Funny thing is if you watch GT's review of Skyward Sword, even though they give it a 9.1 or something when you listen to the review, it sounds like they want to give it a 8.0 or something. But in honesty their criticism of the actual game are pretty spot on.