>ditch the obligatory dungeons that have been in the series the past two decades
We do not need dungeons when the focus is entirely on the overworld secrets and interactions.
>expand on the crafting mechanics
Fuse is a really interesting mechanic that provides considerable utility, but I think it can be built upon still.
>story needs to be back at the forefront despite the openworld sandbox
It's incredible to be able to go anywhere and tackle the game in whichever way you want. There should be more stories to be told in the various locations throughout the world.
>world expands due to choices and actions
Tarreytown was really cool, but it was a one off thing and there wasn't enough choice involved. Players should get to choose where a town might spring up, have a role in shaping it more directly, and farther choices made when the town is established.

Two game ideas I have for Zelda would be a survival sim with crafting elements, and an Ocarina of TIme reimagining that brings along climbing, fuse, and crafting in an open world.