Trying the n3ds core "Citra" in Retroarch, is that not working? Launching game either from Retroarch or Emulationstation just crashes back to Kodi home screen.
Followed the requirements as seen here: New Core: Citra (Windows/Linux) – Libretro to no avail.
n3ds works out of the box, no needs to change retroarch options for me
the only requirement is to have a decrypted rom
and without logs we can't help you more