I don't care either way. I'm leaning more toward not allowing them, but I can see why people would like to see them in the cities. However, SE needs to figure out the right way to do it. No speaking to NPCs while on a chocobo, no entering buildings, and noone is able to check your bazaar while you're on your chocobo.

What I do have a problem with however is that it could be incredibly distracting/in the way. If I'm in the city trying to craft and someone lands their chocobo right over me and makes it so I can't see my crafting sphere anymore, that would be insanely annoying. Yes, I could always move, but it's something I shouldn't have to worry about while inside the city. Those are my only reservations about it though.