how long are we willing to say took place b/w the ending of SS and the backstory to TotK? b/c TotK's legend says the zonai came from the sky w/ the sacred stones and that's how hyrule was established, which just feels really off when it doesn't mention that people descended from the sky first w/ the whole triforce itself and it had to take until a random never before mentioned species to make hyrule, not to mention how primitive the early TotK hylians looked compared to the skyloftians, like what even happened?
Things feeling off to you subjectively isn't really an argument I can respond to. If we look at the timeline then the kingdom of Hyrule wasn't established until after the Triforce had been sealed. That an external tribe was necessary to establish Hyrule is an assumption. We don't know why (in this hypothetical scenario) the Hylians didn't establish Hyrule right away. They weren't exactly a large sprawling civilization in SS though. They were a simple people. I'm not sure what you mean with the Hylians looking primitive, we only ever saw them during Rauru and Sonia's rule. They were wearing Zonai inspired attire (guards were wearing armor you can find in the game). They were far from primitive since Totk is literally all about the advanced technology of that era.
the rito's existence in TotK's backstory makes zero sense, so they just came to be after SS yet had to have died off before MC, only to have an explanation to why they came back in one timeline branch (WW) and then just...randomly show up again in another? (BotW) which does NOT work b/c that means tulin and the current rito couldn't be descendants of that rito b/c they needed to have been alive for all that thousands of years, but we've never ever even seen mention of them in any other game
You know, this is not on you personally because I see this everywhere. It's amazing to me how Zelda fans are simultaneously all about world building and lore, yet act like there is no world outside of the kingdom of Hyrule. We know shockingly little of the extended Zelda universe. The idea that the Rito could only ever exist as a magically induced evolution of the Zora is a headcanon that the fandom has mistaken for canon. I'm not denying their origins in Tww, those were made very clear. But where does it say that the Rito has never, and could never, exist as a separate species in the larger world? Where does it say that they were something that Valoo specifically created out of thin air? Not to mention that, while the Koroks are identical, the Rito are very different from their Tww counterparts. I don't have proof either, but I think it's a mistake to be so rigid about the lore.
we were supposed to believe that OoT ganondorf was the first one, which obviously can't be true now if TotK ganondorf existed during the earliest time of hyrule, but does this mean during the entirety of the series besides SS, he's been there under hyrule castle this whole time? as in during certain games like OoT, WW, TP, etc., there were two ganondorfs? one of which could've been awakened at any time? imagine that
It's honestly not impossible. In Japanese mythology it IS possible for a spirit (or their equivalent to one) to inhabit more than one body at a time. Think of the hero's shade being the hero of time, containing the spirit of the hero, talking to his descendant (who also contains the spirit of the hero). What's interesting in the flashback with Ganondorf in Totk, is that 2 gerudo women behind him have writing on them which translates to "Koume" and "Kotake" respectively. This is certainly conjecture, but I wouldn't say it would be outside of the realm of possibilities that they found a way to plant the demon king's spirit into a new body. Think about it, they're 400 years old and why did Ganondorf need surrogate mothers that are known to be scheming masterminds in favor of demons?
as for the idea that TotK's hyrule is a brand new different hyrule from the previous one which was destroyed or who knows, nothing in the game really tells us how that's the case besides all these inconsistencies, unless a developer flat out states it, we're left with a backstory that just cannot coexist w/ what we've previously known
So despite all of what I've said, I do think that it being a new Hyrule and a clean slate is what's more likely. If Nintendo were ever pressured into giving an answer, this is probably what they'd go with. Like you I don't like it. I agree that it would've been better to just reboot the series in that case.
Until they shut me down though, I will fight for the alternative theory. It would go well with the Zonai being the interlopers as well as the city in the sky.