Okay let's start:
First I'm a musician and I would LOVE to see a real orchestra playing the music, that would be AWESOME!!! They say that it's difficult to implement but it's not actually, you simply make like a player with say two tracks; Hyrule Field On Foot and Hyrule Field Underwater. They are let's say 2:10 long (and repeat) and are 100 bpm. Okay. You make them run at the same time but one is silent and the other plays... You see, like that, when you jump into the water you can change the volumes to switch to the water variation and maybe change the tempo... It's not very hard to do (music players all around offer these functions)... I hope it's clear though. Mario Galaxy did it, and Zelda simply HAS to be BETTER than Mario Galaxy!
Change the geography:
Okay don't throw bombchus at me, let me explain. Let's start with like the basic. Ocarina of Time's map. There's the kokiri forest east, Lake Hylia is south and all that but expand upon it! Like what's on the other side of the desert? The game forces you in an enclosed area with cliffs as walls, make them disappear, let me free roam the world. I want to cross the Death Mountain area and see the land behind! I want maybe to be able to get to Termina through the lost woods, get to Calatia (yes it exists search for it, it is semi canon info) through Death Mountain Range. I want huge lands, maybe not just Hyrule Kingdom, maybe the whole continent! Of course there has to be full of Towns, and a population to fit it, where are all the towns from Adventure of Link? Kakariko and Castle town seem to be the only ones that pass through the times, it's a shame for a 'Kingdom' called hyrule and has a population not over 150...
As for the time aspect, that would be great if we had a Weekly schedule, upgraded from Majora's Mask. People would have a life and not wait for you to speak to them once and then you don't see them ever after. You could have like an instrument to control time (maybe the time could be taken of the current time of the Wii's internal Clock). To say, change the day, make it faster, slower and even alter weather conditions (not just rain please). In the schedule, some random events could occur, like a certain shop could have a sale on wednesday randomly (not every wednesday) some could be bi-weekly, you know, make diversity. Also this adds for more lasting side quests... Like imagine if you see a merchant in castle town going to gerudo outpost and he wants you to help carry the goods, then the shop would have more stuff (not infinite supplies) and could then offer lower prices. If that merchant got killed, then the stuff would be rarer and thus be more costly. You know create an economy. Those stuff could happen randomly and maybe reoccur further in time! Have people buy goods. That would be a truly immersive game!
Also better the concept of inns, like don't you ever feel weird that Link never needs to rest? It's okay but it would be cool if after say 3 days without sleep he'd be less efficient and needs rest at an inn, also when taking humongous damage and restoring could not recover all, he could take a break. That would be a bit more realistic.
I'd like a multiplayer option, like we could have some minigames and stuff to do with friends. Don't throw bad and unfinished stuff to us, just imagine. A horse race through Hyrule Field, you get the choice of Link, Ingo, Talon, Ganon, Zelda and else... Then you compete in the race, the winner gets rupees you have bet in the race... You see that would be an opportunity to tie the single player with multiplayer... Aslo, there could be Capture the Flag kind Games... You start on Hyrule Field and Each team (of two) spawns in a area, you get to capture the other team's flag... Or even do that in a dungeon! That would be really cool to me! Mixing the Single and Multiplayer! Or there could be 'deathmatches' like you choose from a set number of characters and you go in an arena which can be anything, like a Dungeon, the Castle, whatever, then you compete and use your weapons and tactics to get the other player's hearts to zero and win! I would definitely love that! Link and Ganondorf fighting for real (player wise!!!) Zelda could do magic like in Super Smash, except in a Zelda styled mobility (not 2d movement). A gerudo gard would have a spear and Dual Scimitars... That would Definitely make the game longer lasting! Imagine a Link's Crossbow training but better as a multiplayer option! That would be AWESOME! I would really like to see better multiplayer in Zelda, the DS games are not bad but they're not enough. These ideas could be added as seamless single player switch to multi game, adding great replay value!
Speaking of Replay value, let's add quests that can reoccur, like saving a town from Moblin Invasion or getting stock to shops... Carrying letters... I don't know, make me want to play even if I killed the last boss, that could be the time to make me use all my items in a very fashionable way, just be creative! Of course pieces of hearts are fun but they age too, add something new. Let me play as Zelda or Sheik, just for fun! (That's so cool is Super Smash, they should definitely put it in there).
The Dungeons, here they go, I love dungeons, make them less and longer, WAY longer. Like, don't just make a mid-boss, item, then Boss... Add different areas, Don't make it linear, I want to come back to it when I have other items, I could go deeper and fight maybe another Boss which could give me a non essential Item but cool nonetheless, like a different shield, armor piece or just something fun to play with. Make them really more deep and filled with stuff, treasure and stuff I'll have to come back to get... Make bosses on the Field too! Dungeons are cool but puzzles could be also made in the overworld, like in a deserted town, which is basically the overworld, where you have to learn what happened and complete it like a dungeon, keys open buildings that contain more stuff and there you go! Just make dungeons interesting enough that I'll want to come back to later. Also temples are supposed to be a place to worship deities, there should be people worshipping there or at least guarding... I hope you catch my drift.
I have more ideas but I have to go now, maybe I'll post more later. I hope you like it, at least some part of it!