In Wind Waker we see how in it's history we have no Hero when Ganondorf was released(the fact that they mentioned Hero of Time means that he should still be alive when Ganondorf freed himself). Also that is just life sometimes. You make a decision thinking it is the right thing to do in the heat of the moment and later come to regret it. In BotW this happen when the King of Hyrule of 10,000 years past banish both technology and order the Shiekah back into hiding. His actions caused the birth of the Yiga clan.
In TP as you know the Ganondorf got that Triforce of Power yet the Sages didn't know why. They probably were not aware of what happened when it comes to time travel since Link traveled back before he even first met Princess Zelda. Ruto and Nabooru were both mentioned in the game and was tied to the naming of the Divine Beasts themselves(Vah Ruta after Ruto and Vah Naboris after Nabooru).
Saying nothing connects is false and you know it. I have been playing Zelda games since the first game on the NES. Also the fact that you mention Fi contradicts you previous sentence.
Ruto was mentioned on the tablet located around Zora Village. It mentions her being a Princess who awoke as a Sage and was celebrated by the Zora(in which one of the Divine Beasts Vah Ruta was named after).
In Twilight Princess, none of the events of OOT were ever mentioned.
It stood on its own. And again, it worked much better that way.
Wind Waker directly references the events of OOT at the beginning, so yes, it's a sorta sequel.
So the connections the game implies make sense.
Breath of the Wild however, stands on its own, again.
With none of its lore connecting to other games.
The only exceptions being Fi (though only her sound effect is heard) and the Easter Eggs and Cameos.
Easter Eggs and Cameos however are just that.
They are not meant to be taken that literal.
Kinda like the Stan Lee cameo's in the MCU movies.
As for Ruto and Nabooru: They are obvious references, yes.
But then again, it wouldn't be the first time in the series, where characters have the same name, yet are different entities.
The prime example being "Impa".
Each any every Impa in the series, is NOT the exact same character.
Same is true for both Link and Zelda.
Even in Majora's Mask, we see characters like Koume and Kotake returning as friendly characters.
But they're not the same Koume and Kotake from OOT.