At some point somewhere, they said that they weren't planning to put any other third party characters in Smash Bros, and the only reason Snake is in is because Kojima begged for him to be in Melee, but didn't get in, and the new lead guy seems kinda loose about the whole project.
And I just really don't like the idea of Sonic in Smash Bros. Youtube would be flooded by kids with "OMG sonic or mario who winz?" videos. As if the sprite fights aren't enough.
Also, giving NiGHTs and Sonic places in the game open up the field for more crappy characters that look cheap in-game. I guess all the horrible fake "SSBB New Charcter Menu" with a thousand crapy obscure characters in it have really put me off the idea.