I dont see the problem. I use a controller had have 4 hotbars, 5 if you include the default one I have shared across multiple jobs/classes. And 1 is just a whole bunch of macros. For my SMN and SCH it can be a pain when trying to control the pet but eventually I just set up macros for them too.

Then it came down to just knowing the hotbar and muscle memory.

Now I can see a problem if come 4.0 the pets get new skills and I get new skills and have to redo some or all of 1 or 2 hotbars and redo some macros. But I did that with 3.0 and it only took me less than an hour to fully change them, and after that a couple of dungeons to get used to the hotbar.

However if you have quick reflexes you can manuever through your hotbars and macros with ease. I prefer the controller setup because it gets annoying having all of my skills just sitting there on my HUD taking up 1/3 of the screen.