Famitsu not long ago caught up with Nintendo about the SNES Mini and they spoke about how Nintendo chose what retro titles would make the final cut. It was revealed that popularity, units sold and audience familiarity was ultimately taken into account:
Famitsu How were titles chosen for the Japanese and Western versions of the SNES Classic Edition?
Nintendo It depends on the game’s popularity, whether people were familiar with it, and the number of units sold. We carefully hand-picked each title to ensure the game lineup appealed to a large audience, so it makes the SNES Classic an easy purchase.