To be fair I don't remember what exactly pointed to the City in the Sky and Skyloft being the same, but I remember that it was a thing. source: dude trust me
Even when it seems like they're their own thing in the game upon release, those ideas often make it into future games and there's where...
That's not necessarily true. Connections do exist. I've seen some pretty convincing theories that the wind tribe from Minish Cap became the Rito in BotW, due to similar imagery and naming conventions associated with both (the new Rito symbols and the name Tabantha for example), and I'm like 90%...