It has been a long time since the first citizens of Bottlecap Bay arrived... but from what we know, yes, it was coordinated. There were about fifty Pokemon who established the city originally, and more followed after - although most come in boats, even if they can fly or swim. It's a long journey, after all.

[From where? Polteageist might not know themself, although they'd be hesitant to admit that.]

My understanding is that air- or water-borne Pokemon are fairly uncommon, in general. It may be reflective of the world outside of our city, although... it's hard to say, since we don't hear much news from out there.