One issue that occured to me that you didn't address is how the overworld is structured. The 3D zelda games, for the most part, seem to have one large, open central area with other small areas branching off from that. This results in a few fairly isolated area with limited, well-defined connections between them (if there are connections at all). The central area is relatively empty and boring, with a few token enemies and fences and maybe one complex in the middle, but mostly empty space. Travelling between areas is a pretty well-defined affair, you either go to the hub then go to another area, or you travel through a specialized passageway like big door or a tunnel. There was never any doubt or ambiguity as to what area you were in, no transition zone that had some features of one area and some features of another.
Most of the 2D games, on the other hand, had a lot of interconnected areas with trees, hills, rivers, and other obstacles that prevented you from going directly from one place to another. Besides Zelda II they didn't really have a central hub area that just served as a a way to get from one place to another, traveling directly between areas is just as easy and common as traveling through the center (except in cases like LTTP where you couldn't travel through the center at all). They tended to have transition areas between environments, like a rocky area with some dry vegetation between the planes area and the desert area, or increasing density of trees before you get into the forest.
I would much prefer to see a return of the 2D overworld model. No more isolated areas, it is just one big world map. There could still be a fire area, a lake area, and ice area, and so on, but rather than being fully separate areas, they would flow into each other, with numerous criss-crossing paths leading between them. Many of these paths would need items to access or open, but once you get the necessary items moving between areas without going through the central hub area (if there even is one) would become the more common approach.
The central area should also not be just a big open field with a building in the middle, either. It should have a much more complex environment with large groves of trees, rivers with bridges, hills and cliffs, random buildings, valleys, and areas you can see early on but can't access until late in the game. It should actually be an environment with things to do (in addition to a few token treasure chests), rather than just a way to get from one area to another. It shouldn't necessarily be the fastest and easiest way to get from one area to another, it should be sufficiently complex, time-consuming, and dangerous to cross that players want to find more direct routes between areas.