Hey, y'all!
Just wanted to add here that, imo, by far the easiest way to play on a controller is by using steam input!
Simply install the game, add it to your steam library (+Add a Game button in the bottom left of the steam window, Add a Non-Steam Game..., then navigate to Beyond Good & Evil), then right click>Manage>Controller Layout, and voila! You can remap it yourselves, or you can click on "Browse Community Layouts for games without official controller support", then navigate to "COMMUNITY LAYOUTS" and download my layout called BG&E PS2 Controller layout, which matches the PS2 controller layout almost exactly.
Have fun!