I think they should just go ahead and make a "Nintendo Universe" game, where you scan in your amiibo and he/she/it becomes a playable character like Skylanders just with different play mechanics. I suspect such a game is already in development actually, but they'll start amiibo by using Smash first.
Eventually they have to make some kind of "hub game" IMO because what happens for example if they want to make amiibos of characters outside of just those that are playable in Smash? It won't work because your amiibo won't have anything to do if they can't even be a trainee character.