I'm not saying I'm for or against the idea here, but assuming there IS a redesign in the works for the cities in addition to zones, there's nothing to say that they can't add some kind of a freight elevator in Limsa Lominsa that lets you move your chocobos around inside. Personally, I don't really see a huge benefit to having your bird walk around the city. I think that I'd much rather see NPCs in a place like Gridania riding chocobos around while patrolling the town, and that's about it.