We have updated the game to solve some of the version 3.0 beta issues. If you want to play with a controller, please download Version 3.0 beta via the link below.
Right now you cannot play version 3.0 beta with anything other than a controller.
Please note that once you have installed version 3.0 beta you can still continue to play version 2 with mouse and or keyboard. Save files work on both versions.