Well, like I said, Chocobos are being nerfed for 2.5, so you shouldn't have nearly as much of an issue with them then. Really, the key to easy fights in KO (and KO Critical Mode when it comes out) are Protect/Shell/Regen/Poison. They last nearly the entire fight, and can really make your life easier. Not so much against Chocobos, but in other tricky fights.