Would be great to see more puzzles not isolated to rooms, so puzzles linked up across the whole dungeon or landscape. Really need better use of items too, combining multiple items in succession, and possibly having dual functions for certain items.
Hopefully the landscape will also be more organic and less marked out. For example if you step into the dungeon where you get the hookshot, it's almost instantly apparent that you'll get it there.
More item use/puzzles in the overworld would be great too.
Side quests that involve some puzzle solving would be great too. Game needs more sidequests and NPC interaction in general; Skyward's sidequests were shit.