For Tanks, I can't speak how things work with a controller. For DPS, However, you can put what you need for a given battle in 16 slots. There are 8 hotbars (7 is you don't include the one with all the red buttons) at your fingertips. For one of those, you can have your main rotation skills, and on the others you can put what you need on a per-battle basis.

As a BLM, I have my Thunder 3 for procs, fire for procs, fire 3, blizzard 3, transpose, swiftcast, rage strikes, flare, conversion, limitbreak, freeze....that takes care of any rotation I need right now. And I haven't needed to go into another hotbar yet.