The lack of permanent rewards severely hurt this game. Everything you need is given to you in the beginning and all your meaningful rewards are given to you through shrines and divine beasts. Collecting everything, doing all the side quests, and clearing enemy bases don't get you anything of value other than materials, rupees, and weapons you don't need.
Doing these things don't feel necessary anymore and that's due to the lack of permanent items. One thing I never understood was why the bow or even the magic rods break. The boomerang also felt really useless as a long range weapon. So why not make them permanent weapons? They could start out weak and be upgraded as you go on. The arrows can be shot farther, do more damage, and shoot more arrows at a time. The magic rod could be toggled between fire, ice, and lighting, shoot more balls, do more damage, and your magic meter could even be increased. And the boomerang could start out wooden, then be upgraded to stun enemies, become razor sharp, and lock on to a great number of enemies. The korok leaf could have also been a permanent item serving as a tool to solve puzzles and travel on rafts without taking up a weapon slot in hopes that you'll run into a raft at some point.
Bottles should have been limited but also something you get rewarded with for various side quests. There could have easily been 10 total and would have felt a lot more satisfying to earn since it's both useful and non-disposable, making the trouble worth your time. There's also jewelry you get in the game with different functions in the gerudo town. Rather than taking up clothing slots, these should have been rewards and also been permanent upgrades to Link just like the silver and gold gauntlets in Ocarina of Time. They could have even made some special grip gloves as a permanent upgrade that prevents you from slipping off mountains in the rain.
A simple reworking of things like this would have greatly benefitted the game. I get what they were trying to do with the custom, disposable, and physics-based aspect of the game, and it's very welcomed, but at the same time, everything else was kind of simplified as well that they didn't really leave the rest of the game with much to work with because they focused all their attention on the new elements.
While the world is massive, the bulk of the game comes from shrines, divine beasts, and korok puzzles. Everything else is just there to give you something to do as a distraction from finding shrines, korok puzzles, divine beasts, and memories. They badly need to flesh out other aspects going forward and make the entire experience rewarding.