You might be able to experience MSU-1 enhanced games on the new 3DS using
PinBox.
Emulate the game on desktop snes9x and then upstream the video output to the 3DS. I think PinBox has wireless controller setting, too.
As for the sound, use bluetooth headphones.
I know it's not really emulating on the 3DS itself or travel friendly, but that's the only way I can think of at this moment in pulling it off.