Alright problem solved. The problem was with the emulator that RetroPie uses as the standard SNES emulator. To fix the issue I switched to using the pisnes emulator. Here’s how:
Scroll all the way down till you find the part referencing SNES
Below the COMMAND line there is a list of alternate emulators.
Highlight and copy the line that says: COMMAND=/home/pi/RetroPie/emulators/pisnes/snes9x %ROM%
Now replace the entire command string above with what you just copied.
Save the file.
Now navigate to:
Scroll down to the Joystick section to modify the controls. They were way off originally. I basically just matched it to the retroarch.cfg mappings, and removed the extra functions.
Not sure if it was necessary, but I added buttons for a second controller in this file:
# Get codes from “jtest /dev/input/js1”
# from package “joystick”
Scroll down to the graphics section
“DisplaySmoothStrech=1” to 0 (this made the games blurry)
“MaintainAspectRation=1” to 0 (fills the screen)
That’s it. Now emulation station opens SNES roms with PiSNES instead of PocketSnes. Confirmed that it has fixed 2 player issues at least with Super Bomberman. Hope this helps some people!