I have to agree with most here and say that BotW is already a great game, and it will be hard to top it. I'm not sure if my opinions will make the game actually better for everyone else, but these are some of the stuff I'd like to see on top of BotW formula.
Improved battle mechanics and enemy encounters
Wind Waker and Twilight Princess provided variation in your attacks. They could add more like a counter (thanks, Return of Samus), and a sliding move (thanks, Horizon). These are entirely optional but would make for fresh enemy encounters. Relevant to this would be having better boss battles. I can't help but think Skyward Sword had more variety with its bosses than this game.
The return of standard equipment
1. Hookshot - Can make climbing much easier/faster given the right surface or you can upgrade it so it can stick to different surfaces
2. Musical instrument of some sort - Can be used to control weather/day cycle, unlock some stuff, etc.
3. Some device or item that lets you see the environment in a different light - Minish cap made you small, Bracelet in LBW made you stick to the wall and travel the Dark World, etc.
Less micro-dungeons, more big dungeons
I know that completing all shrine quests is entirely optional, and it's a nice change of pace to discover these areas every now and then. However, after completing all the mini-shrines in my normal difficulty run, I was thinking they might have gone overboard with the quantity. The 4 beast dungeons are great but those are it, only 4 dungeons. I think that's the lowest number of big dungeons in a Zelda game.
Other stuff which might be controversial:
Actual water levels - I really liked exploring Lake Hylia's floor in previous games, just diving, equipping the iron boots, etc.
A companion - I'm currently finishing Steamworld Dig 2, and I realized that having a companion is not really that bad as long as it's implemented properly - same like Fen. Since we're talking about a game after BotW, I think the return of a companion will be good.