Brawl is not an advertisement to whatever a third-party wants to promote at the present time. If Capcom is represented in the game, they have one character to do that with. Resident Evil is popular but its characters are not. If you honestly believe that more people in general will recognize Jill Valentine or hell, Nightmare over Megaman, then you're in denial. If sales were all that mattered then they would be getting Madden to do commentary for each match.
Capcom is not out to represent a single series, they have to represent the entire company. Megaman, even if sales aren't that great, is still better known to the general public than the actual company name. It would simply be the most beneficial choice to make for them, and yes, I'm talking about the business aspect of this.
Plus this game is pure fan service, and as its been argued, this is Nintendo's game. The third-parties are just along for the ride. Even if Capcom DIDN'T want Megaman (and didn't like money) it's not like they really have much choice in the matter. This game is going to sell like crazy, like bat-**** crazy. It's not going to matter if Capcom is repped in this game or not, it will still sell like mad. Even if they didn't want Megaman, Nintendo really isn't going to give a rat's ***. And just by looking at the polls (if you even need to, common knowledge should be a enough) Megaman has the support. More than any other Capcom character. Bar none. You cannot argue that, and if you do, please find the proof.
And that's worse case scenario. So you want to argue the business aspect of all this? There you go. The fans, at the end of the day, are the business. Megaman is the face of Capcom. And it would make the most sense to have him in, as many many many people have said before. Stop being so stubborn and use some common sense.