A custom firmware like luma3ds. You need to be on 9.2 or have a9lh. You need to download the .cia version and you should get 50ish fps. I think you need both the .cue and .bin both named the same and then boot the .cue file.
(you can get near full speed with cia version on new 3DS, by disabling Audio/video synch (Settings>Audio>Audio Sync Enable OFF and setting sound resampler (Settings>Driver>Audio Driver>Audio) to "Nearest")
Got that from retroarch thread here.