As someone who played the majority of SMN on controller before switching for HW, it really comes down to what is comfortable for you, which will differ per player. For example, do you find it 'easier' accessing the left side of slots (LT/L2 + D-Pad & Face Buttons) or the right side? Do you prefer using the DPad while moving or the buttons instead? It's those kind of questions that can influence where you put your skills.

For me, general rule of thumb was: GCDs on buttons, Aetherflow skills, Pet Commands and Buffs/oGCDs on D-Pad. Certain exceptions had to be made though. If there's skills you always use back to back, place them next to each other, and so on.