Just because Roger was the Pirate King, doesn't mean he was invincible. Maybe Roger didn't beat Aokiji, but then again, neither could Luffy. You know the saying. "He who fights and runs away."
Anyways, Rio could be the name Clover was about to say (Oda's a total c**ktease), but until it's finally revealed, I won't worry about it. For all we know, Skypiea could've been that city literally blown sky high by the government (or they just escaped to the sky).
And sorry, but "It's not a cool enough name" is a lame rebuttal. I almost wish Oda would do that later on just to spite y'all.
From what I've seen in the anime, I would guess that the civilization was centred on...
In Franky's flashback, Tom and Kokoro are discussing the island, and Tom says that Water 7 is going to be abandoned and forgotten if something isn't done. Kokoro says that it's be too bad, as it's the island that once DEFINED AN ERA.
Large part of the island is underwater. It seems that the houses are not just built on pillars - there are actual building that submerged a long time ago. In effect, it might be a good guess.