This thread seems to have veered off topic.
Sea CITIES are lovely for those of you interested in futuristic mods, but COLONIES (ie, the ability to gather offshore resources) is a somewhat distinct matter, and a severe limitation of the game (IMO).
Personally, I think it more important that we have the ability to snag luxury and strategic resources from the water tiles. The game designers' omission of the "sea roads" was catastrophic, effectively disabling half of history.
Can't we concentrate on working around this?
Sea colonies attached to land roads is one good idea put forward.
And yes, minimalized sea "cities" acting strictly as colonies has merit. But it would require a graphic different from cities in order to be representative of its purpose in all but futuristic eras. So I don't think that'll work elegantly.
If someone could convince Firaxis to patch true trade roads, at least for the water tiles, then we could live happily ever after. Sea commerce would work, piracy would work, and that other half of history could finally be simulated (I found the suggestion on CivFanatics' cover page, that the game has educational merit as a sim, to be laughable... JMO).