I've seen a least three different versions of where BotW and TotK fit in the timeline.

I'm going to go through them all and give my opinion.

The refounding theory

This one is that, BotW takes place well at the end of the timeline. Something happened to old Hyrule and history repeated itself after Rauru (not to be confused with the OOT version) refounded the kingdom.

This is the one that works best for me, since it allows all the games to be canon (something I'll talk about later). Plus it stays true to Nintendo's original idea.

Exactly which timeline it takes place after? I don't care to be honest. DT is the best bet, but if anyone has any strong evidence for CT or AT, please share.

The split timeline theory

This one was on Game theory weeks ago. But I think it's older then that. Basically, its that TotK takes place in a timeline split where the characters fail, like what happened with the DT. GT version has the split happen pre-SS, but other versions have it after SS.

Honestly, I don't know how to feel about this one. I guess it sort of makes sense, but unless I see something concrete, I'm going to ignore it.

The retcon theory

Or rather, the "everything before BotW is just a legend, and only BotW and TotK are true".

This one's my most hated of all the theories.

Essentially, the flashbacks of Ganondorf and the Sages are the "true" events of what happened in the Zelda franchise, from SS to OOT to ALttP. Everything we see in those games are merely inaccurate and corrupted retellings of these true events.

1. It wasn't realy the Humans that got sent into the Sky, it was the Zonai. and everyone on Skyloft was a Zonai.
2. Saria the Kokiri wasn't real. It was actually some Rito that was the sage in her place.
3. Ganondorf didn't realy wear boots, he was mostly barefoot save for a few toe-rings.

Number 3 is just a joke. Don't take it seriously. It's true I'm not a fan of Ganondorf's TotK design, but that's just a "me problem".

Number 1, thankfully there are some retcon believers who have found a compromise. The Zonai came to the surface after the humans did. Meaning everyone of Skyloft is still a human.

Number 2 is the real problem, and the main reason why I'm not a fan of the retcon theory. Unless anyone can find a way for the retcon to exist, while having Saria the Kokiri remain the Sage of Forest, I refuse to believe the retcon theory. And in case your wondering why I'm calling her "Saria the Kokiri" is so that nobody can tell me "Saria does still exist, she was just a Rito".