two things that helped me:

You can set the hotbars to only scroll through say 1-3 when weapon out, and other with weapon sheathed. Its in the character config->gamepad menu

Also for arcanist based jobs, you can disable the petbar and put any pet skills you want to use on a normal bar.

These fixed pretty much any issues i had with accidentally using skills, and with switching quickly between bars. It also takes some time to get used to gamepad, its a new way of thinking and if you werent in beta or didnt use this before give it time.