The following comes from an IGN interview with Masahiro Sakurai...

"Just because the game is being cooperatively developed with Namco Bandai involved, that doesn’t at all mean that they’d be given any special consideration for having characters in the game. Smash Bros. can still be considered as an all-star collection of Nintendo characters. Just like with Mega Man or any other third-party character, it would have to be a very special situation.

Adding third-party characters should be considered a very special case. In the last game, when we added Sonic and Snake, there were lots of different hoops to jump through as far as getting approvals and making sure all the parties involved were happy with the way things went. You can consider it a very special circumstance for that to happen. Even in cases like adding Pokemon characters, there are a lot of parties involved and there’s a lot of wrangling. It’s much tougher than people can imagine. I know lots of people have requests and their own ideas about third-party characters that would work, but I want people to understand that adding a third-party character like Mega Man is a very special situation."

This was followed by a discussion from IGN about adding Pac-Man. This is not something Sakurai said was happening, but he did discuss what it might be like if Pac-Man appeared.