I actually think that each third-party company will wind up getting two characters in the game...two from Sega, two from Konami, and two from Capcom (though Mega Man hasn't yet been confirmed). I have no basis for this claim, other than the idea that Sakurai's list of considered third-party characters from way back had at least one "classic" character from each company (Sonic, Simon, Mega Man) and one "new" character (NiGHTS, Snake, Viewtiful Joe). Now, some might argue that Snake is a classic character, and indeed this is true; however, Snake didn't really get noticed in the mainstream until recently. When Metal Gear Solid was first announced, no one went out and bought PS1s because of it (not until after word-of-mouth had spread). Simon, Sonic, and Mega Man were instant stars.
Like I said, I have no solid evidence for his inclusion. However, I do think it would be a damn good idea.
At the very least, he'd probably make the cut as an assist trophy (not perfect, but I'll take it, I guess).