Turn off the pet hotbar.
It's not nearly as hard to control the pet as it seems. My main hotbar is filled with heal actions, including pet skills, but I have only one pet command on main hotbar, which is 'Place'. Second hotbar is filled with attack skills of my own, along with white mage additional skills that are nonessential for scholar in the heat of battle.
Overall, the preparation of hotbars for any class on controller is a matter of "What do you think you will use the most?" and "What do you use while moving?" With those in mind, you can figure out what is most important to put on face buttons and what can suffice on dpad, and so on.