Doubtful. No matter how many third party characters get added in, Nintendo is still running it, and I find it highly unlikely that they'd let their works get totally outdone by third party groups.
Second, they didn't kick out characters to make room for third party characters, they kicked out a boring retread and a couple unbalanced characters. Doctor Mario should never have been in. He was a pathetic excuse for a character, being essentially a carbon copy of Mario. Pichu was too broken to play. And Mewtwo got rebalanced into Lucario. You want more Nintendo characters in there? Fine, we've got a couple hundred Fire Emblem characters and Pokemon to go through, who cares that 90% of them would play identically. They put a lot of thought and effort into all the characters that went into it and I'm sorry if your favorites didn't get into it but I highly doubt that Krystal would have made it in had Snake and Sonic been pulled. Nintendo wanted the game to be fun and appealing for the most people possible, and I think they did just that. Nintendo has thousands, if not millions, of characters, and the vast majority of them had no chance of making it in. Yeah, some of my favorite characters were left out too, but I prefer to just enjoy what we have rather than whine about what isn't there.