I had a lot of compatibility issues with the injector and with VirtualNES (this game literally crashes it). RetroArch works with this and a couple other games just fine for me. My original 3DS is too slow on everything except for QuickNES, but a new 2DS or 3DS may be able to use whatever core.
This is the guide I used. Trying to install through the Universal Updater seems to not actually install the application...