I recently installed RetroPie on my Raspberry Pi 3 and everything was great until I tried to use two USB controllers at once. I plugged them both in and configured them, but when I entered a game, neither controller would work.
After a lot of debugging, I found out that if you start the Pi with one controller plugged in then plug the other one in after Emulation Station has booted they will both work in game. So if you're having trouble getting two USB controllers working at the same time, try that.
I haven't tried rebooting with them both plugged in after they both worked, but that would be ideal. Being able to just leave them as is and turn on the Pi then play would be great.
I also want to try out these SNES style controllers:
I'm tired of using Xbox controllers for games that don't fit them well.