Ok first off, part of this is a little beyond SE's control, but official drivers for ps3 controllers on the pc.

That said, better functionality with contollers would be nice. Targeting is a bit of a chore, even with the new feature. You should be able to map gathering/synth to a keybind (ie press x to start gathering/synth) being able to open inventory and gear with button presses would be nice, instead of clunky menu. And last of all an item use function for contollers. I use a controller to play and most of the time am not able to use items in battle (health potions, enemity reducers) because of the lack of a use button. There are several functions that are currently mapped to the controller I never use (target lock, auto-run, change view, and view status effects).