I fought with prime hack for a while trying to get it to work. I was using the GameCube Metroid prime 2 iso.

It loaded fine, but I could not get the controller mapped correctly.

I discovered that there is a Wii Metroid prime trilogy iso.

I tried this one and then suddenly everything worked perfectly.

The on screen button icons even matched the steam deck instead of showing the GameCube button.

I hope this helps as it’s a great series and it deserves to be played through primehack.