Before I get started, I am fairly impressed with BoTW overall, but the following points have definitely diminished its staying power.
-the generic fantasy overworld
It might be the biggest, most convincing Hyrule kingdom yet, but BoTW makes you trudge through the same environments you've explored countless times since A Link to the Past. Forests, deserts, volcanos, snow mountains, fields, you've seen it before, and the repetitiveness of the overworld undercuts the sheer impact it ought to have, and could have had if the game used more creative, more abstract environments, which I would like to see in future games.
-the excessive inventory
The inventory system is a collector's dream, or if you're like me, a plain nightmare.
First, let's talk about armour, which is what I would label as cumbersome game design. There's a reason why the games have progressively done away with multiple tunics. For example, in SS, you can breathe underwater once you get the Water Dragon's Scale, removing the need to ever enter a menu and equip a Zora's Tunic. In BoTW, you are constantly going back and forth from the menu, changing your clothes - because you need to scale a waterfall, or because there's a thunderstorm, or because it's cold. In the process of doing this, I would always forget to change back into defensive gear, and getting hit with three times or more damage was always annoying. Not to mention, outfits come in three pieces now. In future games it should just be the green tunic.
Second, the enemy drops have gotten a bit ridiculous. They are also frustratingly designed, because they do not add automatically to your inventory; you have to physically pick them up. This is a big problem because of the high cliffs and the sort of 'bouncy' nature of a lot of enemies when they are knocked away. If there's something I hate, it's when I beat a difficult enemy, but they go flying off a cliff when defeated, and I go climbing all the way down to get it, and when I'm climbing back up, it starts raining.
-weather
Rain is always something of a catch-22. When it rains, it's harder to climb, so you'll want to pass time by lighting a fire. Except the rain will put one out. And it's not always possible to find shelter to light one either.
-enemy variety
There really is not enough, as people have said. I would like to see something fresh and exciting from future games, rather than more Bokoblins.
-the 'sidequests'
The game labels everything as a sidequest, when really, a lot of them are not sidequests, just giving them something you already have in your inventory.
-the flat, unmemorable score
The score for BoTW is very disappointing, aside from a few tracks. Most often, you hear the same piano notes over and over. Really boring, and easily the weakest overall soundtrack of the 3D Zeldas.
-there is no story, no lore, no enticing villain, no triumphant ending
Which is perhaps the most disappointing; I could forgive a lot if the story were more interesting, more emotional, more cathartic and less retrospective. The emotional weight of SS inclines me to forgive a lot of negatives in that game, for example.
On the topic of weapon durability, I do not share the same problems as everyone else per se, and I think it was fine for one game (if it shows up in the next game, I will be annoyed). I do think there were too many weapons, however. (Why did we need different bows, for example?)