1) The Overworld: This is my big one. When I was a kid playing the original Zelda, what captured me was the absolute sense of exploration; wandering from screen to screen, not knowing what lay next. Sure, there were some limitations in the exact routes (not having a raft/footladder, etc.) but for the most part, the whole map was accessible right from the beginning. This meant easy areas next to the first temple, and areas like Death Mountain where you got your ass handed to you... and the only way to find out your limitations was to go to those areas.
This has not been captured in a Zelda game, probably since LTTP and I would argue that even there, there were some serious limitations d/t the light/dark mechanic. This was distilled even further in OoT, MM, and TP. Essentially, the Overworld is still not only a hub, but you're constantly ushered in which direction to go. What I want more then ANYTHING is a fully breathing overworld; I want to be able to go into areas where I shouldn't go to yet because I'm not strong enough. I want to have that sense of exploration, and trepidation going into an area. I want to be gently led so I feel like I found it myself as opposed to having a character say "YOU'RE GOING TO THE ICE TEMPLE NOW."
I think WW actually did this pretty well; the Overworld was huge, and I did feel like I was exploring. Unfortunately, the challenge wasn't really there, and uh... the entire map was water. I would LOVE to explore a Hyrule full of land, lakes, snowy peaks, deserts, forests, multiple villages, ruins and oh yes... palaces that was comparable to the size of TWW. That would seriously be my dream game.
Other things:
2) Utility of Items: TP introduced some really cool items... the few times you could use them. What use was the Spinner aside from using it in the Arbiter's Grounds, a few times in the Overworld for a few pieces of heart, and the last temple or so? the Dominion Rod? I'm glad that they introduced so many, but I want them to be more then glorified keys to get to the next part in the game. Hell emulate LTTP and introduce some completely optional items to the mix.
3) Music: Orchestrated, and let Kondo and Yokota do it. The dynamic music thing was worked around in Mario Galaxy (Bowser battles, going underwater, etc.) And even if it isn't exactly what they want, I think that they give more credit to it then how actually effective it is. This shouldn't be an issue at this point.
4) Voice Acting: Like most people's wishes, everyone but Link I would hope.
5) Temples: This is the one area where I think Nintendo is on top of their game. If they keep up the quality that they had in TP, I'd be happy.