Okay, to start out, I'd like to say that TP was a very good game. I know lots of people like to complain about it being too much alike OoT, but it really was its own game at the same time. Despite its being a good game, it does have its flaws, as does every game.
First thing I would probably change concerns the Spinner. It was an awesome item, as I'm sure many would agree. It had one flaw, though: it wasn't used enough. Okay, so you used it in Arbiter's Grounds, and you even used it to get a few heart pieces. But it wasn't used beyond that. There are items, such as the Bow and Arrow, which are used in multiple dungeons, since they're all-around items. The Spinner could be much the same, if Nintendo allowed. It was a very good item idea, but it didn't get enough use.
Another thing I have a concern about is the Slingshot. It felt very tacked-on to me. You used it very little before the first dungeon, and then it became useless. Just another item to eat a slot in your inventory. Worthless!
The Magic Armor is another thing that needs to be fixed. I liked it. I mean, it could be used to get rid of money so you could get that chest in that dungeon that would otherwise be forgotten about. It was useful in situations in which you had tough enemies to face (such as floor 49 in the Cave of Ordeals). Yet, it had one flaw: it was treated like an armor upgrade rather than an item. This means you had to equip it like armor, which involves hitting the Start button, going over to it, and hitting the A button. Same thing to dequip. Now, if it were treated like an item, it would be a matter of assigning at a button (Y or X) and hitting that to equip/dequip it. A lot easier, don't you think?
My next complaint has to do with the hidden technique, the Great Spin. You charged it and unleashed a powerful spin attack. Cool, right? Wrong! You had to build power, and then be at full health, to boot! Not only does this mean you'll almost never use it (come on, when was the last time you were full health in the middle of a dungeon?), but it's a pain to execute, as well. If it didn't have that full health requirement, it wouldn't be nearly as bad. Or if it still had that requirement, but expanded on all your sword attacks. Either way works for me.
Now we move on to the Helm Splitter. To do this move, you had to first Shield Bash, and then hit the A button (I do believe, it has been awhile though). How about, instead, we get rid of the Shield Bashing part? Instead, maybe we hit A, then B in mid-air. It would be a lot less of a hassle to use, right?
Another thing lots of people have noticed about TP, is the lack of strategy involved in the boss fights. They are all simply too easy! I died maybe once at Zant my first play-through, and once or twice at Ganondorf (the fight as a whole) my first playthrough. Pathetic! They're the final two bosses and I didn't even break a sweat deafeating them! Gohma (or whatever the Temple of Time's boss is) was easily the easiest boss of them all for me. Again, no skill was required at all. You simply find the working strategy, and apply it until the boss is dead. Nothing at all to it. This also ties into the enemies.
The enemies in TP weren't hard at all, except for the Dark Nuts. They, unlike others, required thought and skill to beat. They actually hit you once or twice, and it hurt. In other words, they were awesome. The other monsters, however, were poor. Their AI is incredibly stupid and needs work, as does their placement. Maybe have them ambush you out of nowhere? Maybe place them in an area that will benefit them, but not you? Come on, Nintendo! Where's the challenge?
Both of the above two things could be fixed with Difficulty Levels. With this, we could have hard-core gamers, new gamers, and regular gamers all be happy.
Another big complaint I have is Zant. He was a terrible character at the end! Nintendo did a good job making him out to be an evil, powerful guy who needed to be stopped, until the end, when he was just revealed to be a whiny, pathetic, over-dependent brat. I was hugely disappointed with his turn-out. I really do believe he had a lot of potential, and Nintendo ruined it!
EDIT: The post below mine has reminded me of some other things:
Personally, I liked Wolf Link. It might be that I'm biased, since I love wolves, but it seemed to work for me. For one, the senses was something new and unique that added something to the game, in my opinion. I liked how the scents were implemented, how you could dig for rupees and such, and even that you could see otherwise invisible creatures. However, the wolf also had its flaws. For one, his attacks lurched you forward, bringing the possibility of leaping right over the edge. Another thing is Midna's cheap attack. It was a one-hit KO to the Twili monsters, which goes back to what I said about enemy difficulty. Now, I don't think it was a bad attack, just that it was overpowered. If, instead, you had to weaken the enemies first, and then go in for the kill, it would have been a lot less cheap.
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.
The Double-Clawshot was a major disappointment for me. I went through the City in the Sky, thinking it was a cool dungeon, bound to have a cool new item that I just couldn't wait to see, and I find another Clawshot! Granted, this opened up new possibilites the normal Clawshot didn't, but I just can't help but think that someone else (such as Barnes, maybe even Fyer) could have made that for me. Yes, I'll give that it's cool, but certainly not cool enough to have its own dungeon, when another item could have been there.