I'll suggest some of the more obscure awesome 3DS games:
Shinobi
Rhythm Thief
Code of Princess
Liberation Maiden (download only)
Cave Story 3D
Tales of the Abyss
Mutant Mudds (download only)
Dead or Alive Dimensions
I would also recommend Sonic & All-Stars Racing Transformed over Mario Kart, but I've heard the 3DS version is weaker then the other versions so I can't yet.
Also, while they aren't exactly obscure, Kid Icarus, Fire Emblem Awakening and Mario 3D Land are AWESOME.