3 Cities... a Desert, Port and Forest. Yeah seen this, its called Bastok, Windy and Sandy.
You can easily simplify things if you want to. But, really, I bet most people fall into one of those categories. Either, they want to start out in the middle of a forest, or maybe on the oceanside, or they think a desert would be 'new and interesting'. Having it limited to three cities (unless the city in the mountains shows up as a starting location) did give me a similar feeling, and being experienced with FFXI, making the connection was easy. But I think SE is simply striking at what people identify with. The fact that way
more people started out in San d'Oria compared with Bastok and Windurst is testament to that. For some reason, people identify with a castle in a forest rather than a 'technological' desert city or a rural tree-based city.
Then, ****, if they had announced a city deep in the canyon, an island city, and a city built on top of a giant tree (see: Cleyra
:p), people would still make the connections. "Oh, look, a tree! Well, Windurst had a large tree. That's just a Windurst copycat!" The fact that certain people debate whether Gridania is closer to Sandy or Windy proves this, to a strong degree. Some say Ul'dah is very close to Sandy, when others say because it's in the desert, it must be a 'Bastok-clone'. All cities will have some similarities to each other. But instantly making the connections is crude and premature. Architecture, surroundings, and people / government make a city what it is. Most people consider just a single aspect, and with that, any connection can be made.
Additionally, as some have brought up, having fantastic cities in the beginning just makes expectations all that much higher. Like someone said, "If Bastok were Sea, getting Sky would be far less special." If the beginning cities are this fantastic, having a floating city or something entirely unique later on is almost to be expected.