As an N3DS user you'll find that all the main Snes emulators have their quirks, pros and cons. You might as well make use of all of them.
- Snes_9x for O3DS has good compatibility and great features easily accessible from a nice UI. It's fast and works great on N3DS.
- Regarding the Retroarch cores found in stable 1.3.3, PocketSnes can run a couple of the special chip games better than other options, and Catsfc is a superb and accurate all round performer. These options have the most features.
- Snes VC is accurate as well, but lacks the high compatibility of the other mentioned emulator options. It's also tricky / not possible to import game saves into it. It does however have instant usability in terms of having specific titles ready to dive into from the home screen, and most common games run perfectly on it.