Skyward Sword was the first Zelda game that became tedious to me rather than becoming more engrossing the more I played. I love the idea of reusing environments but there has to be some sort of effect you've/time has had on the area like in OoT. Dungeons weren't memorable. Music wasn't memorable. There was no satisfaction in finishing off one of those harp melodies correctly. The motion controls weren't terrible... it just wasn't as much fun as it sounds like it should be. For one thing they were used in places they shouldn't be e.g. turning the keys to fit the doors. And for another there should be more bosses like Ghirahim which require you to be an excellent swordsman but along the way there should be mini-bosses which teach you a certain technique that will be effective against them. e.g. I found I hadn't learned anything about effective feinting by the time I got to Ghirahim and had to figure it all out there. The lack of engrossing sidequests. The ability to fly was something I didn't look forward to at all in game. That shouldn't be possible. I blame it largely on there being nothing to do while flying, nowhere to go, was there a sidequest to race people other than the Wing ceremony? Combat would have been difficult to design with the motion control as it was. I could go on, as an overall experience SS wasn't fulfilling like the rest of the Zelda franchise.
I wouldn't mind some motion control in the new Zelda, but I do think it would be stupid and not likely that they don't use the gamepad as the main controller in the first Zelda U game.
Anyways, I feel like most things on this list would be a great move forward if they were done well.