When playing an RTS one of the key factor is the speed. I believe (and I hope...) PA will add hotkey support to the game. I find myself very confortable with the grid preset (like starcraft 2) where: Code: Q W E A S D Z X C matches the UI buttons. Will PA have something like grid preset hotkeys?
Considering that PA's orders are in a vertical line, I don't see how this would be any degree of useful. However, I do agree that it would be more ergonomic to have all the buttons in a grid fashion and set the hotkeys as such. I currently have mine set up like so - Q - Assist, because it looks like G, for Guard W - Patrol, for Wide Berth? I don't know. E - Reclaim, for Eat, stock key R - Repair, stock key A - Attack, stock key S - Stop, stock key D - Move order, D for Drive F - Fabbhurrs 10 points if you can guess what my favorite coop game is.
the fact that the buttons are vertical (or horizontal) isn't much a problem Q W E can be assigned to the first 3 buttons. A S D can be assigned to buttons from 4 to 6 Z X C from 7 to 9 or something like this
Settings > Keyboard Rebind anything to anything. Except mouse axes, but I have no idea why you would want to rebind mouse axes in an RTS.