They are minor support companions. If we gave them super features, the bots that are already abusing them in their current state would love it even more.
There are better ways to combat bots that don't negatively affect the gameplay for other players. What decisive advantage does a chocobo give a botter anyway? I have a hard time believing that it's so huge that it warrants making the system as bad as it is now.

As it is now, I don't feel like the trade-offs for having the chocobo out are worth it, therefore to me the system is useless.