I think that's a great idea, thought about this too, users could release scripts for it too.
but wouldn't it be easier for say a nes emu, first, though?
I mean compatibility is important but that's features like that that would make me want to play 8-16bits games on that POS 3DS screen, it's cool to be able to play on 3DS but I own a phone, a pc, psp, 360, PS3, wii etc, snes emulation is good there, I could play regular snes games on snes too, but extra and unique features is where it's at, at lease to me.