To make a mugen full game that has a story mode witch you sometimes fight people, then sometimes you go throughstages(like SSBB's subspace emirassy)
I've never played SSBB's subspace emirassy, but I would say "yes its possible"If you are able to make Bonusstages like Bane84 did with his Super Mario Bros. level for example.Then put Chars and Bonusstages in the right Order.