Korok seeds, weapon durability, rain, four dungeons, crappy bosses and empty overworld...
Do you agree that it seems to be easier to point out BotW's flaws than it is with previous Zelda games given the new elements it brings to the table and the new design choices?
What one person sees as a flaw, another will appreciate. For instance, some people will praise the 3-day gimmick in MM, whilst for me it was just one more feature I couldn't stand in the game. So going through your list...
Korok seeds - yeah, the number is blown up too much, the tracking ability of the Korok Mask was hidden behind DLC, and I dislike that only about half the amount leads to anything useful - at the same time, this seems more like the norm with Zelda games with very few games actually doing collectables completely right (though before anyone says it, I do agree that with BotW being the newest game, they should have done better) - I can think of one instance where a Zelda game really did collectables right, and that was ALBW with maiamais. Up until the very last one you received something worthwhile for your effort. But most Zelda games tend to task you with collecting way too much of something and you either get a crappy reward for it, or it's practically useless by the time you actually manage to collect it (every single time I played OoT I couldn't be bothered to even try getting all Skulltulas).
Weapon durability - I get that some people hated it, and some people loved it (using it as an opportunity to do double damage). For me it just was a non-issue. It was never a struggle to fill up my inventory, in fact I more often struggled with deciding which weapon to drop to pick up the new one - so freeing up a slot or two actually became a good thing for me.
Rain - yes, this one I wholeheartedly agree with. Rain always was an annoyance, and was the only weather type I did not find any particular way to take advantage of, unlike for instance lighteningstorms where I could take advantage of nearby metal items to control it. I do wish they had thought out better ways to make rain a feature rather than an obstacle.
Four dungeons - I do wish the beasts had more meat to them and been more different from one another. But I don't find the amount to be a problem, not with the heaps of shrines out there, several of them long and intricate, giving me plenty of puzzles to solve. I do wish they had done fewer strength challenges, not done blessing shrines that could be found without completing a proper challenge, and made sure any shrines they had properly ramped up their core concept so that they didn't come off as way too quick and simple. There's definitely a lot of improvement that could have been done, but I really enjoyed a lot of it as well, so it's not a major issue for me.
Crappy bosses - If you're talking about the different Ganon incarnations, then I wholeheartedly agree with you. It would have been much more interesting if for instance we ended up fighting corrupted versions of the champions than just one more barely different version of the endgame boss. The overworld bosses, however, those I loved.
Empty overworld - this is where I'm going to disagree the most. I found the overworld of BotW to be the most engaging out of all the Zelda overworlds I have played. Even with the option to ride horses, I found myself constantly choosing to walk instead, as I kept wanting to stop and check something out, climb something, pick something up. Yes, a few areas here and there had less to do, but the vast majority was packed to the brim if you just bothered to look. I was constantly engaged when I explored, there was always something I wanted to do and pretty much every single time I got distracted on the way by something else. In my opinion the overworld was the best thing about the game, and what made it my favorite game of the series.