I'm a pretty big fan of the way BotW is structured; the freedom is hugely welcome. That being said having only four main dungeons, each of which are short, about the same difficulty wise and bland visually was kind of a let down. It'd be nice if the next game had more dungeons, each of them more traditional Zelda and themed differently, and I think a Link to the Past's sort of structure would help with the difficulty (or lack thereof) woes; the game's dungeons would be split off in like two blocks wherein at the beginning only like three dungeons are available, though they can be done in any order. The early mid game would then open up into more dungeons that were previously gated off in some way. These would present more of a challenge but can also be tackled in any order the player decides. While more variance in dungeon structure would be ideal, the increased focus on "Puzzle Box" style dungeons should be retained, if perhaps not for every dungeon.
Additionally get rid of the shrines; content wise they range from decent to pointless and boring, and as such are too inconsistent. I think instead having like 12 more substantial mini dungeons with good rewards at the end would go some ways to ensuring more consistently good content as well as more varied visual consistency. They would also be more naturally incorporated into the environment and thus make the game's world more engaging than BotW's empty feeling (tho imo the emptiness does work in the game's favour) and sometimes kinda uninteresting game world.
I think this structure would also help with telling a story more set in the present era of the game as opposed to the past like in BotW. While I love the way BotW's story is presented it can feel kind of uninvolved in what the player is doing at any given time, so a return to a slightly more linear story wouldnt be a bad thing. Each area's story would be self contained but at the end contributing to the overall story of the game, like BotW, meaning that the player ideally feels no pressure to get to each part of the story in any order or with any particular pace.