I am the last person who I thought would come in here and defend Chocobo Companion (one of the most broken, unfinished features in the game), but I will say this: you should view your chocobo from the perspective that anything it does is a bonus. Don't rely on it like it's an additional party member. It's not going to keep you alive in dire situations, it's not going to interrupt key enemy skills, and it's not going to dish out a ton of damage. But when you have a chocobo out, battles are just that little bit smoother. It's worth having the chocobo out when you can, but if it were any more effective it would either be overpowered, or SE would have to start designing open-world content under the assumption that you have a chocobo with you -- and we don't want that.

I made the mistake of trying to make my chocobo a tank, which as it turns out is not a good idea. It can't hold threat at all, even against the most lackluster of White Mage damage. But it makes soloing FATE boses and Hunt marks a lot easier, just having something else constantly whacking away while I take a break from damage to take care of HP upkeep. From what I hear, a balance of mostly DPS with a few ranks of Healing is the way to go with Chocobo Companion. But even then, don't expect an ally who matches your own power in any way. Anything the chocobo does is extra.