I know I will get flamed for this, but these are just my two cents. These are not what most people want and I already know that.
First of all, I do agree with the majority of posts here. Some of the most unique items to ever be in a Zelda game were also the most underused items as well. The dominion rod, the spinner, even the ball and chain needed a lot more screen time. I personally WISHED so badly that I would stumble into some secret rollercoaster-type course designed just for the spinner anywhere in the game but alas, I never found one, save for the small one in the dungeon in which you found it. I even went back to the dungeon at one point just so I could use the spinner in that one place, because it is a very fun item! It really is! The same goes for the dominion rod: it is fun, but the thing is you don't use it enough, and it would be nice if they gave it more screen time imo. I personally wished the ball and chain to not be USED more often but make it less heavy and so unwieldy so that I could use it in an actual battle if I ever wished, because It's just awesome smashing an enemy with a ball and chain but when it's just so difficult to use it really does take the fun out of it.
I also wanted the combat system in Windwaker as well. I loved the fact that you actually could have different combos besides the "stab stab stab STAB" combo or the "front slash - front slash - front slash - FRONT SLASH" combo that honestly could get repetitive for me after a while. Still, I love Zelda, I loved OoT and MM even though that's the extent of their combos it was still fun, but that was then and this is now. I'm not asking for Zelda May Cry here (I don't want 75 hit combos, don't get me wrong), but in WW, for example, the combo system was dependent on how you tilted the control stick. Even though that is a very lazy way to make different combos it was something. It was different. I don't remember if TP had different combos but if it did, then they weren't as cool to use as WW, which disappointed me. It shouldn't be hard designing different combos for different control stick inputs; just maybe one or two more combos, that's all, for some variety. I would also like to change the helm splitter too. One person said make it so you press A then B in midair and personally, I think that would be perfect, seeing as the neutral A is already a lunge. All in all, add new attacks as you progress and make the combat system just a bit less shallow.
Another thing I always secretly wished for ever since WW (They really did a lot of things right with that game imo) was secret dungeons. It'd be nice to have some mini dungeons after you beat or even before you beat the main ones in the story to go through and have fun with in your spare time. The secret dungeons don't have to be amazing or special, but I'd like it if they took some time and putting some kind of a boss in them would also make me happy. I personally want secret dungeons with secret bosses and secret items you could get. Knowing Zelda team, they'll probably just put in Piece of Hearts in the secret dungeons but... I dunno, a bottle, some kind of new item, anything would work for me besides the usual Piece of Heart.
Some things that really disappointed me with TP were the lack of screen time for Epona and the boring Wolf Quests. When I got Epona in the game it was so... not dramatic. In fact, I barely needed her, since I could very easily transform into Wolf Link and run or warp to wherever I needed to go to. Even though Wolf Link is not as fast as Epona, you still get the point. If you put Epona in the next Zelda game, try not to have Wolf Link making her obsolete, or at least make us do something as crazy as in OoT to save Epona.
The Wolf quests.. Ehh, I'm not going to lie. When I played them for the first time, I did not say to myself "God this is boring" but when I think about it, I can see that they really did slow the game down for me, as well as other people. Give Wolf Link more attacks. I mean, you had over 4 YEARS to work on this game! It shouldn't be that hard to think of something for Wolf Link. Midna being able to attack is a step in the right direction, but giving her a one hit KO attack is plain lazy. You can use wolf claws, you can have chases with Wolf Link, etc. It's okay if you can't make one on one combat funner, make Wolf Link do different objectives instead for fun.
I also would personally love a return of the parry attacks from WW, but again, that's just me.
Another thing that I (and others) have come up with is the possibility of Werewolf Link, as opposed to Wolf Link. He would be a lot cooler, it would make more sense that people and Gorons be afraid of him, and his attacks wouldn't send him forward. The senses would still be in the game, he could actually use items like this, and it would fit more with the theme TP had.
Uh... Wolf Link was already pushing it pretty badly, and turning him into Werewolf Link might be taking it too far. I don't see how he would be cooler, that's just a matter of opinion, though his attacks would be nicer and easier to use. I may be biased after seeing SEGA recently failing at turning their blue hedgehog into a werewolf and failing badly, but I don't see how Wolf Link would be cooler in any way.
Though, despite all of what I said, playing the Sun's Song and turning the day into night just to have Link transform into Wolf Link would be very awesome!