I wouldn't be surprised if we saw some major changes in the city affiliation system. For version 1.xx, it seems as though Grand Company affiliation has supplanted city of origin in terms of giving your character a locality with which to identify. This may mean that city affiliation is going to work differently in the future.

There was an interview or a post by Yoshida a really long time ago in which he said they were working on some kind of system in which you would move from city to city as you leveled, eventually choosing a "home base". (I'm sorry, I don't have the patience to go looking for the post/interview where this was discussed.) Perhaps he wants players to be able to experience all of the cities before choosing one (as is the case with the current Grand Company system).

I think there's a fair possibility that the game won't begin with us choosing a home city at character creation. Before anyone gets angry, please understand that I'm not arguing that this will definitely happen, but I do think it's possible.