When you are in free mode or attack mode, when you first hit the mob, your chocobo will follow your line of fight. It's then up to you to move 180º so AoE Cones like Morbol's Breath won't affect him at all.

I don't know about your Chocobo Rank, mine's Healer 9, and he saved me often enough, myself being PLD Main when out doing solo fates and/or beast tribes.

OP - You have my vote. It would be nice to see 2 man + 2 chocobo into dungeons, giving them a real purpose.

Then again, I would also love it to get our minions to at least fetch the loot.. sigh..