One tiny change to the story structure that I would make

Most Zelda games can be broken up into two major chunks. An opening where things are established, followed by a big event leading to the main goal of the game. In Ocarina of Time, you collect the 3 gemstones and then you become an adult, leading to the rest of the game. In Skyward Sword, you travel to each area and beat a dungeon, then Zelda and Impa have to flee, then you do the rest of the game by revisiting those areas. Etc.

In Breath of the Wild, you take down the four Divine Beasts, or not, and then you can go straight to Ganon and finish the game. There are no distinct phases. Just one. So I was thinking about something that both would break the game into phases and also fix the ending somewhat, which a lot of people have a problem with.

Maybe the first time you go to Ganon, he is too strong, and Zelda, in desperation, transports both of you out of the castle. The second phase of the game is where Ganon has been set free since Zelda is no longer containing him, and so you have to travel around with Zelda following you to free all of the villages again from the malice. This time it's not the Divine Beasts who are corrupted, it's the towns. Every town is covered with that sticky goop and the residents are corrupted by it like Naydra was. Link and Zelda must free the towns by purifying some kind of source of the race, which would mean going through a more traditional dungeon, maybe with the help of either the Champions or their descendants again as well as Zelda.

This way, we could also work in Korok Forest and Kakariko Village as being affected, and the game would be longer and there would be more dungeons, and the moment where the lasers fire on Ganon would feel earned because he would still seem strong to players since they couldn't beat him before. These were the biggest complaints that people had with the game.

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