This is definitely not a complete fix, but this update will enable PS controllers and likely others to work in the game. If yours still doesn't, try searching for Set up USB Game Controllers in the Windows start menu, click Advanced and select your controller as the Preferred device. I'm working on a more complete overhaul of the input system, which I hope will provide even broader support and eliminate any workarounds. But time is an enemy to us all. If you hit problems, please contact me.
Hope you are enjoying the journey!