You can find the autopilot under "misc" at the end of the list.
About the key layout, I will see what can be done. I just wanted to give you an example of where it could become problematic as things are handeled differently.
I still hope that there can be the "choose the layout yourself" option so everyone can decide what he wants.
As for the mouse controle. I just fired up WC1 and our current build and they are pretty much alike. There is still some issues but I hope we will sort these out.
Gamepads are supported as far as I know even if the support isn't the best to my knowledge.
The coders worked on it but as the request for these was never very high it hasn't gone very far.
Thing is I can't test it myself as I don't have a gamepad.
Also it will be interesting on how to get all the controles on a pad. Never thought about that.