I think that with the way chocobo companions work right now, this wouldn't really work. You can build your choco with any combination of skills. I've chosen to raise mine as a healer, and I always put him into healing stance, but he's still not a great healer. Plus, chocobos do not know how to dodge. They just stand there and get hit with things like Bad Breath. I hear that tanking chocobos aren't very good tanks. Or they can have a blend of skills from all 3 trees, which doesn't really help anyone.

I like the concept of a chocobo-assisted dungeon. But I don't know if the execution of it would really be possible. Maybe once we can re-allocate chocobo points.