Zelda lore
I really don't like how BoTW screwed up the Zelda lore by taking place in all the timelines, despite all the contradictions, and taking place over 10,000 years after the previous games. But TotK somehow made it worse.
First off, why haven't the Zonai been mentioned previously? I expect the first King of Hyrule to be Skyward Sword Link or a descendant of him, not some humanoid goat. Also, why are the Rito in the early days of Hyrule? It's already bad enough that BoTW implies that the Rito existed in all other timelines, while also coexisting with the Zora. Now apparently, they've been there since the beginning.
According to the ZeldaWiki, they're talking about the founding of a different incarnation of Hyrule. Well, that's great! The Hyrule we tried to revive in BoTW is not the same Hyrule we all know and love. Up to this point, the only other Hyrule we knew about was the New Hyrule in Spirit Tracks. And why did a non-Hylian decide to re-establish a kingdom that he has no ancestral connection to? It doesn't make sense. It's called Hy-rule, as in "Hylians rule".
Seriously, BoTW and ToTK might as well be reboots of the franchise, at this point. None of this makes any sense.
I also don't find the excuse that giving BoTW a set placement in the timeline would've limited the creative freedom of the development team. They could've easily made an open world Zelda game set immediately or a few centuries after Zelda II because Zelda II's overworld is huge, possibly even bigger than BoTW's/ToTK's overworld, and for whatever reason, Nintendo has never made a chronological follow-up to Zelda II even after over three decades. It would've been much easier to go with that route instead of fucking up the lore again.
https://zelda.fandom.com/wiki/Zelda_Timeline#Arrival_of_the_Zonai
Zelda lore
@xianc78 Hyrule is more like "hylia's rule" than "hylians rule." there is a lot we still don't know about the Zonai, but legends and such refer to them as gods, so perhaps hylia was a Zonai as well.
Eiji Aonuma has stated it does take place at the very end of one of the timelines, but never revealed which one. He's the guy who came up with the timeline to begin with so I'm assuming he isn't just talking out of his ass.
My interpretation of botw/TotK in the timeline is that it is perhaps a more unified timeline in 2 ways.
1) many zelda games are, in botw's lore, simply legends. Perhaps glimpses by sages into different realities and perpetuated as legends.
2) many zelda games are inevitable, regardless of timeline. They all will happen at some point and it will all happen over and over again.
Perhaps Zora lived elsewhere, beyond Hyrule. This is alluded to in TotK with the idea of more domains than just Zora's Domain that exist out of Hyrule. It's possible that some may have evolved differently or not at all depending on their geographic location and timeline.
That is to say nothing of the koroks, but that one is more easily explained. Deku Tree turns them into sprites to protect them from Ganondorf before Wind Waker, so it stands to reason that he would do the same before breath of the wild at some point.
I definitely agree though that the story was only made more confusing and it doesn't really respect itself. It tries a little too hard to be the "smash ultimate" of zelda games, so to speak. The only game that surely exists as more than mere legend is Skyward Sword, given the existence of Fi inside the master sword. Perhaps Ocarina of Time as well, but we can't be too sure that those aren't just legends either.
Zelda lore
@xianc78 one can hope we get some explanation at some point on where the game is in the timeline because it's a clusterfuck right now.
i think TP could feasibly be a prequel to ALttP. the downfall timeline was a way of saying "this is everything before we had an idea of what we wanted the overall story to be" because after ocarina they actually had pretty clear ways for the story to go. it probably would have been better to not include those games in the timeline at all, give them their own place, because it doesn't make any sense that two timelines would be spawned due to time travel with one timeline being a purely hypothetical one. the downfall timeline is pretty much the "non-canon" timeline because of that. it would have been better to say those games were only canon to themselves, and that ocarina of time essentially was a reboot.
which could be basically what they're doing here with BotW and TotK, but it's made more confusing by the fact that it still references all of the old games and even uses common terminology like "the imprisoning war" despite it being a completely different war from the imprisoning war we had known before.
the story of botw and totk is serviceable by itself, but trying to fit it in the broader zelda mythos makes it seem pretty poor. i'm still looking forward to see how the zelda lore youtubers try to fit all the puzzle pieces together, though, or at least what they have to say about it.
tears of the kingdom reminds me of kingdom hearts 3 in a way, in that the fans hoped to get a lot of things about the story cleared up after such a long amount of time had passed, but they were only given more things to think about. it's in pretty poor form, imo.
botw/totk is certainly supposed to be a soft reboot. there's not really another way of looking at it.