Mostly from Wikipedia that has the whole "Capcom 5" saga and some from memory either from IGN or EGM/Gamepro at the time. Do remember Mikami's promise of cutting his head off from IGN at the time.
http://en.wikipedia.org/wiki/Capcom_Five
I think the reason for Mega Man and third party character themselves was certain requirements that either the character had to be a mascot-type which fits Mega Man as Capcom's big mascot or has to have a lot of history with Nintendo consoles which really fits Mega Man more than Snake.
In Japan there was a fan voting poll about which third party characters to include which did have Mega Man as the #2 character and then nobody else close to those two. Sonic was #1 overall and I think the poll itself was meant to be used to determine who gets placed in the very limited spots.
http://m.ign.com/articles/2011/05/27...ash-bros-brawl