I am also using itch.io (here's another screenshot, showing the option to choose OpenGL). The only advice I had was to use the OpenGL version since it works fine with my controller, but your mileage may vary. If you click the gear next to the Launch button, you should get this screen. Make sure to just use the OpenGL version if you're having controller issues. Otherwise I don't have much advice for you unfortunately. If you controller works well in Steam, you could use the "add a non-steam game" and launch the game in big picture mode and try it that way, but I don't need to do that.
