Instead of chocobos as mere transportation, why not have them as a class of their own that can ride around and do battle. Your weapon would be reigns or a chocobo flute. When you equip it, you are put on top of a chocobo and you can run around with it and use it in battle. Your chocobo would have it's own special attacks like kick, peck, and choco meteor.
To go along with your chocobo you'd have a crafting class just for it. To "repair" your bird, you'd feed it greens. The choco-crafter is the class you'd switch to to do so. Maybe he'd also build equipment for your bird or things to breed or evolve your bird.