TWW, if you couldn't tell from me siggy, is my third favourite game in the series. If I had to add something to it though, I would make the optional islands bigger, with more to do on them. Maybe add another sidequest. Maybe change the PoH system to 5 hearts per container, and add a bunch. This would make it a lot more interesting, since the islands are all just tiny dots in a huge part of the sea, and they are too spread out. They should also decrease the overall size of the overworld. Not decrease the amount of islands necessarily, but make smaller gaps between the islands so the sailing doesn't take as long.
I would also improve the enemies. Hardly any enemies in this game actually gave me any trouble, which is a shame because they definitely had some potential. They should give the enemies more powerful weaponry, and drastically improve their AI. The enemies were so stupid that I could sometimes defeat even tough enemies like Darknuts without once getting hit.
Although not a huge part of the game, I think they should improve the Nintendo Gallery sidequest as well. Maybe increase our camera's memory space, and give multiple images to the figurine guy at once so it isn't as tedious.
Lastly, I'd improve the Triforce of Courage quest. They should make the challenges to get the Triforce Charts longer, to prove that we are actually noble enough to wield the Triforce of Courage. Not necessarily all combat based challenges, but they should at least test us in some way. It would certainly make the Triforce quest much more fun and entertaining.