This game is one fantastic effort, and I think a few of their flaws are excusable, in that they couldn't have been changed without consequences in other areas. Games truly are intricate networks, and striking gold without a few flaws is rare. Though, there are still a number of easy fixes and missed opportunities I shake my head at.
To start with excusable flaws: my biggest complaint is that total freedom in a video game lacks certain benefits that limits can bring. However, this same total freedom is beloved by so many people, and the giant labyrinth of an overworld that I envisioned in my head would have frustrated many players if they had gotten lost. Such a labyrinth would work better in a smaller world, which of course would disappoint anothet set of people.
Some people criticize the durability system, but it makes perfect sense to me. In BotW its critical that everything points towards helping you beat Ganon, and if you kept everything you got in this game, you would eventually have everything you need early on, and you would have no need to go out and find new things. Other open-world game solve this problem by having more sophisticated difficulty scaling, but those games don't link the main quest to the rest of the game like BotW does. Those games usually make the time and effort it to beat the game pretty rigid. You can either blow through it really quickly like in Skyrim, or you're force to spend a lot of time in the game to level up like in Xenoblade Chronicles. Keep in mind, BotW is not an RPG, and its freedom from the shackles of the XP system allow players to gobble up the necessary upgrades at their own pace. But just in case they gobble them up too quickly, BotW makes sure you're always needing to replenish your weapons supply.
Even the monotony of the dungeon themes can be understood, since the theme made perfect sense. The fact that each of the divine beasts were all the same giant mechanical monster is made up by the sheer awesomeness that these dungeons are... actual giant mechanical monsters! Don't forget the incredible feeling that comes from seeing your dungeon rampage through the overworld, and it just felt awesome to feel liking you were hacking and taking control of it! And Nintendo even went as far as they could by giving wind, fire, water, and electricity themes to Medoh, Rudania, Ruta, and Naboris respectively. The same could be said about your basic shrines, too, as they also contain elemental theming, as well as a number of stand-out overworld puzzles.
There are a few easy fixes, though, and to keep on the subject of shrines, I admit that it wouldn't have defied any reasoning to have a few alternating aesthetics. And while the structure of the story fit perfectly with the open-world go-out-and-find-it gameplay, there's still no reason why they didn't have a more satisfying ending that references the memories, when they already had a two-ending system in place! And lastly, I say bupkis at the Dark Beast Ganon fight. Final Boss fights are meaningless if they aren't challenging.
But considering how big this game is and how new and different it is and how much it does right, it's easy to give these things a pass.