1) Expand combat, specifically the mechanics. I feel like the game very heavily leaned on its parry mechanics to carry basically 100% of its difficulty, and why it's not a particularly bad thing, it doesn't age well into endgame when you're expecting something more interesting and basically nothing different from the rest of the game, except it's "parry this or die".
2) Speaking of which, and i know this is asking too much from Nintendo, but some ACTUAL secret bosses/enemies would be cool. Lyonels get boring fast.
3) Actual locational dungeons. Meaning, not all shiekah shrines, and some actual caves / buildings that are built out as dungeons.
4) Do NOT remove weapon breaking, it literally carries the entire game.
5) Finding/obtaining the Master Sword was one of my favorite parts in the game, because i played for nearly 25-30 hours before I realized I didn't have it and needed to go looking for it. More of that please.
On points #2 and #3, i feel like they could really take some cues from Final Fantasy XV's open world design. In fact, if BotW stole some mechanics from FFXV then it would be an almost perfect game to me.
FFXV things that BotW needs to steal:
1) Nighttime travel actually being dangerous, at least in certain areas. My favorite part of FFXV because if you ever wanted a challenge, you just had to attempt to go somewhere during nighttime and watch giant assholes come out the ground and beat your ass. This would be great in BotW because especially on master mode, the game has a strong survival sense to it.
On that note, they also need to take that mechanic where Magitek Troops start randomly flying in and dropping entire squadrons down on you. BotW kind of does this with the Yiga Clan ambushes, but it's little more than an annoyance because they're harmless. It would be cool if they actually started posing a threat from time to time, forcing you to run at lower levels or have a good fight towards endgame.
2) Completely random, optional, full-length dungeons scattered around the map that serve no purpose other than giving you awesome unique weapons, neat visuals, and a nice challenge. This is important because once you realize that almost 75% of FFXV's dungeons are completely optional, it gives great incentive for exploring the map because the natural path of the game won't take you anywhere near them.
3) SUPERBOSSES......Breath of the Wild had two enemies that functioned this way, the fully-functional Guardians and Lyonels. In FFXV it was great to wonder around and just see these massive creatures that you can fight whenever you find them.
Breath of the Wild has the typical Zelda issue where you completely lose all motivation for obtaining all the hidden gear and maxing Link out because there's literally nothing to test your newfound strength on after you've beaten the game. You can fight the Golden Lyonels and get their gear, but they're the strongest in the game. So what's the point.