My biggest gripes with BotW was:
1. Poor Dungeon design/ they all look exactly the same, including the Champions Ballad DLC Dungeon and lack of Dungeons overall
2. Out of all the bonus armors made available to us, they didn't include the Magic Armor from TP(but they managed to include stupid outfits like the Lobster Shirt from WW) and while I'm on the subject of Armors, not all of them could be upgraded, so it made those particular armors completely useless late-game(which is where you get most of them)
3. After getting all of the Equipment Slot Upgrades, collecting the rest of the Korok Seeds just gets you a huge, golden pile of shit. I felt like they could've at least given us something useful and worth the effort
4. Some of the old items could've been optional, but available(i.e. Hookshot/ Clawshot could've made climbing simpler, especially in the rain. The Magic Cape could've finally made a return as it was only in one game, ALttP, to help hide from monsters and could've had a durability to keep it from being to broken. These are just a couple of really good examples.). One good solution to keep the freedom of exploration available, would've been to implement the ALBW idea of getting major items early on in the game(whether renting, finding or buying, just making them available). This would've fun in theory and in practice.
5. I felt like the Colosseum was kind of a missed opportunity. This could've been a really fun, battle-style minigame. Something similar to the Dark World Tower in ALBW comes to mind here. This would've been a really good way to rack up rare materials/items and Rupees or maybe even some very rare and really good Weapons or Equipment, depending on how good you did and what difficulty you did it on.
6. I totally agree with the people here saying that there should've been a huge cave system/grottos and the ability to swim underwater in the game(I really wanted to swim around the Skull Lake in North Akala for some reason, I don't know why, it just looked like it would've been cool to do.
7. We should've been able to keep and register The Lord of the Mountains after capturing and taming it. Just a minor nitpick here, but still would've been cool to do.
8. The boss battles were lame and monotonous and they reused them too many times with very little variations. The final battle against Ganon really sucked and was underwhelming and I'd go as far as to say, it's the worst Ganon battle in the entire series.
9. The story wasn't very in depth or detailed and felt all over the place since you can regain your memories out of order.
10. After clearing The Trial of the Sword, The Master Sword should've had not just Full Power all the time, but should've had an infinite durability(The Trial of the Sword was fairly difficult and after clearing it, the Player deserved it).
11. After defeating Ganon, we should've been allowed been allowed to keep the Bow of Light.
12. More mini-games and better sidequests with real rewards would've been great. Imagine doing a trading sidequest in a world this huge. It would've been phenomenal!
13. In a world this huge, there should've been a NPC to help the Player figure out what places they had left to visit. It literally took me around 30 hours or so of aimless running around to figure out what place I was missing on the map to get 100%. I was stuck with 99.87% trying to find what ended up being a small bridge that I completely overlooked the entire game.
14. Mekar Island felt like it was easy to miss and could've contained some huge secret, but was absolutely empty and useless. Another missed opportunity here.
15. Lack of a Post-Game. After the final battle against Ganon, the game's ending kind of looks like it sets you up for either a Sequel or a Post Game Story with Zelda. Since I can't remember ever seeing this done in a Zelda game before(feel free to correct me if I'm wrong, but for the life of me,I can't remember a single one)
Those were the immediate complaints that came to mind, but having said that, there was so much this game did give us in return that made it an amazing game overall.
1. Huge ass Overworld, with a ton of shit to do. I can't count how many times I got side-tracked when going to do something and I was never bored.
2. The different types of terrains. From high up Plateaus and Snowy Mountains as well as a Fiery Volcano to Coastal regions and an Island Challenge, Vast Seas, Rivers and Lakes. Rolling Plains of the Akala Region, Flat Plains of Hyrule Field. The return of familiar Regions Like the Gerudo Desert, Lake Hylia, Zora's Domain and my personal favorite version of the Lost Woods as well as new terrain like the Jungles of the Faron Region and the Thunder Plateau, with its unique features( giant mushrooms) gave it sort of a surreal feeling.
3. The return of one my favorite enemies: The Lyonel. This game has, by far, the best, most terrifying incarnations of this vicious beast. Also the only other game, besides Oracle of Seasons, to contain a Gold Version of the Lyonel. Not to mention, it has access to some of the best weapons in the game and should be considered more of an Overworld Boss, rather than a regular OP enemy.
4. All the throwbacks to most of the more than 30 year history. From enemies to NPCs to the somewhat geographically accurate areas(namely the previous Hyrule Market Town on the Great Plateau, by the Temple of Time and Lon Lon Ranch). Also Amiibo/DLC Weapons and Equipment.
5. A new terrifying enemy in the Guardian. Those things were very scary early in the game and it would be a very welcome comeback if it returns in future installments of the series.
6. More back stories/history of the Shiekah Tribe, as well as, the introduction of the rivals of the Shiekah, the Yiga Clan. This was one thing A LOT of Zelda fans(myself included) wanted for years. Getting this was extremely satisfying. The return of a Stealth-based quest, when you invade the Yiga's Hideout was fun too. I can't remember a fun, stealth style invasion of a hideout since the Forsaken Fortress in Zelda: Winderwaker. This was great and these type of quests should return in the future.
7. Back stories on the King of Hyrule, again hasn't been done since Windwaker.
8. Ability to upgrade your equipment using materials. This was a great idea and I'm glad it was implemented in this way.
9. With the freedom to explore whatever you want, the enemies scale to your progress. A series first, if I recall correctly. This keeps the Player on their toes and keeps the Player from from being completely OP against the enemies.
10. The reward of a completionist's dream come true. You get to buy your own house and get to decorate it(although expanding it would've been nice too. I literally would've spent hundreds of hours farming hundreds of thousands of Rupees just to be able to get a little more customization out of this!). Another series first and a great one at that!
11. Even though the Dungeons were bland and overall unappealing, the new mechanic to manipulate the Divine Beasts, offers a new type of puzzle to solve. Even though it wasn't exactly used to its fullest potential, it's still an excellent idea overall.
12. Survival in the wild requires the player to use whatever they can find to survive. Whether it be enemy's weapon, using terrain in creative ways to fight enemies or picking up a stick and pot lid to fight. This all adds to the overall experience and immerses the player into the game.
13. Enemies fight in mobs now. This makes combat that much better, if you ask me.
14. Adding Zelda's Royal Horse, Ganondorf's Giant Horse and Wolf Link into the game. Another few throwbacks that were unique, that made combat fun with better allies.
15. Some of the Shrines and all three of Labyrinths were challenging and fun and I really liked hunting materials from the Dragon Deities in the game(although sometimes their spawns were inconsistant). This made for some great entertainment.
I know this is a bit lengthy and I applaud and appreciate anyone who took the time to read it all. My biggest point here is, for every disappointment this game had, it also had some improvements for. No game is perfect, and BotW is no exception. It is a serious step in the right direction and over the next few core games, I feel like Nintendo will nail it. Breath of the Wild earned the 2017 Game of the Year Award for a reason. It was an amazing experience like none other before it. I, for one, will enjoy this game over and over again for many years to come!