I shudder at the idea of the next Smash Bros or any installment in the future containing less characters. I am hopeful that licensing agreements can be worked out so that everyone returns and we get more characters in the next game. I am expecting a longer DLC cycle as a result, but I am perfectly fine with that.
Hopefully Sakurai saying that a game like this happening again in the future is his new way of saying "this is my last game". There's plenty of big name third party characters and still a handful of first party characters that could make the cut in the future.