Half-Life remake Black Mesa has a Beta for a big update with a new UI and controller support
(www.gamingonlinux.com)
I can't stand FPS on controllers. It completely ruins the game by making quick actions slow and cumbersome.
For example: Half Life and Half Life Decay for the PS2. They had to dumb it down for the controller, adding target lock and auto aiming. Once that happens, whats the point of playing at all.
The haptics on the steam controllers help somewhat, but nothing beats mouse and keyboard for these games.