Trackpad on Late 2016 MBP Stops Working When USB Gamepad Is Attached or ControllerMate Is Running
Fixed

The problem was that apparently installing the new version of ControllerMate somehow checked the preference “System Preferences > Accessibility > Mouse &amp; Trackpad > Ignore built-in trackpad when mouse or wireless trackpad is present”. I turned it off again and everything works fine now. 

Thanks @toma for pointing it out in the comments!