Supply and Demand. The more people and more frequent chocobo's are purchased from a stable the more it costs. The one at Mea is always the most expensive because that takes you to Sky, B.Tree, Mhaura for ToAU and back to Windy itself. Port Jeuno can also be a bit expensive because that's how you head to Citadel, sky and B.Tree. Most others are fairly cheap because they're not rented from as often. Which is why you can usually run to Upper jeuno and get a 1-300 gil bird when Port is 1-2k.