I have issues with the Steam Controller as well. I'll just copypaste the post I made on steam forums.
https://steamcommunity.com/app/353370/discussions/1/3826310674200959836/?tscn=1584124277
ISSUE
When I shut down the Steam Controller using a chord and power it up again, the game only registers trackpad movement for the camera. This can also be observed by powering up the controller for the first time during gameplay and or if the batteries run out.
OS
Arch Linux, KDE
CONTROLLER TYPES:
Steam Controller
CONNECTION TYPE:
Wireless
GAME:
DOOM 2016
CONFIG LINK:
The official config
STEPS
Power up the game
Go in a mission
Shut down the controller
Power up the controller
RESULTS
Unable to play the game through the controller from this point forward
EXPECTED
The controller should reload its config and allow you to continue playing
Nothing extracted yet.
My config: Linux Mint 18.3, Nvidia latest beta drivers 396.54 I believe, GTX970.
Doom 2016 launches fine but the Steam Controller is not recognized as soon as the game starts in its new window. The Xbox360 controller, is however, working as expected.
Another issue: I tried loading the last checkpoint while in game, and it turned into an infinite loading loop, I had to reboot the machine.
Otherwise, performance wise its fantastic!