My hopes and dreams?
Sword Techniques. With all the traveling you do they could implement some sort of optional islands like many in the game that you could earn sword techniques from, it would also populate the ocean more and make sailing less "boring" for those of you who found it that way.
Orchestra Soundtrack. Come on. You all want it. Ever since I heard Skyward Sword I couldn't help but imagine all the great music of past Zelda games in orchestra too. It would be a huge reason to buy the game again for me.
Hero Mode. Hero Mode, in my opinion, was the new game+ that Zelda always needed. It really spices things up. That along with the Gallery would make a second playthrough more than entertaining as the first.
Removed Temples. I disagree with anyone who feels that the story would be broken by more temples. In fact, I think that it could actually fit in pretty well. My first idea is that there could be a larger island behind the ice island that could be accessed later in the game, or perhaps the ice island contains an entrance to the Ice Temple. The other temple could be implemented somehow with Jabun. Perhaps Jabun needs you to retrieve the Pearl, scattered and hidden by Ganondorf's minions? it's really an easy and small adjustment to the story. The overall theme doesn't change much with or without.