I wanna start by saying this game was phenomenal and I loved every minute of it. And when all is said and done I believe it may go down as my favorite game of all time that I've played so far anyway. Having said that, no game is free of criticism, and I can think of a few things that would make this brilliant game even more amazing.
I have a top 10 for a youtube video I'm putting together. I'm leaving out the lack of proper dungeons because the things I list are ultimately small and could easily be added in with a simple patch, but I know that they wont; whereas proper dungeons would be a massive undertaking and not something I could see simply added in, but rather something that we'll likely see in the next Zelda title hopefully on the Switch. So here's my list of what I wish was in BOTW not in a finalized order.
10. (Dual) Hookshots - these fall at the bottom of my list because these would be a fundamental change to the game, something that I think also will be held off for the next game when they mess around more with it. My idea would be to give the hookshots a separate tension meter like your stamina meter that as long as they hold you winds down, and when it hits zero, the hookshot's hold breaks and you fall. This would allow for their inclusion to not be abused to get all over like spiderman (as cool as that would be)
9. Iron Boots/Underwater swimming - this is also a fundamental change, but swimming and exploring underwater has been an aspect to so many Zelda games before, and it can often be fun. I mean shit like the Water Temple isn't great, but adding underwater could add a whole new aspect to the title.
8. Tornados/Blizzards/other extreme weather - we saw a little bit of stuff like this with the sandstorms, but I'd love if shit could get intense, if you're in a bad storm and suddenly a tornado comes by and recklessly throws you across the map. With you're glider, you can survive, but you may find yourself way off course.
7. Fishing Pole and Slingshot - These are two completely unnecessary but all the more immersive items the game could use. We can get fish, so why not give us a chance to properly fish for them, and a slingshot could just be operated similarly to a bow and arrow, but using all the little rocks you pick up along the way. I saw a mod on gamebannana that replaces one of the bows with a slingshot and it seems really great. Unnecessary, but neat all the same.
6. The Windwaker - I'd like if the Toon Link Amiibo could be used exclusively to have brought in this special weapon, it has a 1 hit attack, but that's because you don't use it to attack. You instead hold r and the wind constantly blows from the windwaker in the direction that you blow. This would suddenly make getting around on those rafts WAY more fun.
5. Rune to play that 2D BOTW proof of concept as a fully realized short Zelda top down game - yeah this is ridiculous. But I love this idea, the Sheikah Slate is essentially a smart phone, why not have a game on it that Link can sit down and play. And how great would it be if they made that 2 BOTW proof of concept in the style of the original Zelda into a short 3 or 4 dungeon Zelda adventure complete with save files and everything. I really love this silly idea.
4. Extra page for gear inventory - so this is my first real practical addition here. There are like 4 or 5 too many pieces of gear for the amount of pages they limit our gear to. They really need to just give us one more page.
3. Usage of the One-Hit Obliterator after you complete all of the DLC 2 - let us go back to the shrine of awakening and grab this weapon for the same trade off we made before - one hit kills us, but we get 2 one hit kills and then it needs to charge before giving us 2 more again. I so wanted to go back and hunt down some Lynel with this thing, and was really bummed out to see that we couldn't.
2. Cookbook - everytime we cook a new dish, an entry should be added to a cookbook that we have, so that we can then enter the cookbook, find any recipe we've made before, hit A on it if we have the inventory for it, and your hands will instantly be filled with all those ingredients so that you can throw them in to be cooked.
1. Multiplayer Wolf-play with 2 Switches - If you have a second Switch, you should be able to download like a free BOTW multiplayer client app, that can only connect to a Switch playing a copy of BOTW (similar to the Namco Museum Pac Man Vs. multiplayer app), or if that doesn't work, another Switch with another copy of BOTW. Have both Switch's connect, and one of you play as your Link, and the other gets to play as Wolf Link which they could make a little more robust, adding more control and attacks for a second player to have with Wolf Link.
You put all of that in, and I think that'd be about as close to a perfect of a game as this could possibly get.