NES emulation for a game that uses no mappers, like Super Mario Bros., is 100% cycle-accurate and there is no difference compared to playing on a real console. As for controller, what happens once the final NES controller breaks? They are not being built anymore. Might as well allow any input method now as long as it doesn't do anything the original controller can't. (Setting aside that the communities for some games that require constant mashing of the same button now allow turbo so that their hands aren't destroyed.)