There are a couple fundamental things I would like to point out with using a controller.
The first is utilizing displayed hotbars in order to monitor the cooldown timers on your abilities. The crossbar is insufficient for this since it can only display one set at a time.
The second is mapping out your skills in a way that 'makes sense'. Accessing your sets involves using L or R; L followed by R; R followed by L, and double pressing of L or R. The skills you use the most like those on the GCD should be given priority of access. Furthermore, you will need to assign skills to both the face keys and the directional buttons. Again, priority should be given to the face keys due to ease of access. You will need to use your left thumb for both movement as well as accessing the directional buttons. This means movement is sacrificed for the skills you assign the the directional buttons. Assign them wisely. It will take trial and error to get things the way you want, and striking dummies and boss FATEs are awesome for this.