I've heard that Sonic had been added after the rest due to requests, and the rest of the roster had been completed before then. That's according to someone from Smashboards whom had attended GDC. If what they say is true, then it's silly to say Nintendo prioritized the two 3rd Parties over those specific characters. I think the cut characters were cut for reasons of absolute suckage and lack of popularity rather than to make way for these new, 3rd party characters.