I would suggest this not only be an effort based system but also a time based system. It's not something we could simply hard grind to achieve very quickly, but something that would require a player to spend time with their chocobo and wait for an appropriate amount of time to pass for results to take place. This will give us some very unique individuality to our characters as our battle/mount companions will differ in color, style or ability and the world would not be filled with hundreds of Magitek or very similar yellow birds.

I hope others would also look forward to a more developed system of companion within Eorzea, and just as a side note to SE, you should really allow mounts and companions at the same time.