I don't agree that mouse input is inherently superior. The main advantage is boundless motion, e.g. aiming a gun or controlling a camera. If that is not a major part of the control scheme in a game, controllers are often better.
I see. I have a lot of PC games that I feel control much better with a gamepad. It's a third person action game with analog character movement. In this case an analog stick is far superior than WASD movement/modifier keys.