4. Instanced quests - The chocobo is not allowed in instanced quests such as class or some story quests. This doesn't seem to make a lot of sense. I can use it for all the non-instanced quests and isn't the point of the instance to give me a private/story experience? Then why can't I use my companion?

I really love the chocobo companion and the rank and armor system but right now the functionality seems lacking to say the least.