Using the 3DS as an alternate 2nd, 3rd & 4th controller (for those that have their own already) would be great, except for the little overlooked "fact" that the Café controller is supposed to use Dual Analog and Nintendo didn't see it necessary to put that on the 3DS.
It could still work, obviously, epsecially if it was planned for ahead of time, and it's better than not having a 2nd, 3rd or 4th player because you didn't want to by more dedicated controllers, but it's still a minor inconvenience.