Wind Waker could have been expanded more.
The game is so very linear. Expand the game so you can go where you want to from the start and can actually do things on islands when you want to.
The dungeons are so small, easy and boring. Fleshing them out to make them decent experiences would...
Windwaker could have had more indepth, less trashy dungeons. Also an actual more meaningful reason to all the fishing for garbage spread all over the ocean.