Assuming we get a third game in the botw run, I would love to see link travel back to early Hyrule like Zelda did. Nintendo could use the blueprint of the depths ruins as the backbone for a thriving Zonai civilization. Aboveground would be a truly wild Hyrule similar to what the depths are now. No sky islands as this would predate their creation. Instead we could have a 'dive' feature that lets us visit an ancient Zora, spread out in the waters in and around Hyrule. All new characters (except maybe Raru and friends), but many characters could be ancestors of current characters so they would be familiar in some ways. I would love to see the ability to tame monsters, more complex Zonai devices, and yes, perhaps real dungeons.
Also I could even see a fourth game in this series that totally turns all of the formula on its head. It would actually star Zelda, and she would travel through time to different eras of Hyrule. We'd get to see areas and dungeons from ocarina of time, twilight princess, skyward sword and even many of the 2d titles, redesigned with botw graphics and controls. The focus of the game would be for Zelda to help Link. She must stay out of sight, navigate dungeons to place keys, compasses, maps and/or key weapons that the link of that era will need to defeat whatever evil he faces. I think this would be super cool.