Considering the final Brawl roster was first leaked by a Gamefaqs poster in October 2007, about 3 months before the final game was first released in Japan, I wouldn't be surprised if a place like IGN was able to get some type of information on a new Smash Bros for the Cafe about 6 months before it was suppose to be revealed. Smash Bros is the one Nintendo series where they seem to be unable to prevent leaks from happening.
Assuming Smash Bros has been in the works, its possible that Mega Man's odd exclusion from Marvel vs. Capcom 3 might be hinting toward his addition into another "fighting" franchise.
Don't have a ton of faith in that, but throwing it out there as possibility since Capcom's only statement was they seemed to feel he didn't fit in the game (which was odd, since he was in the first two).
The main problem working against Mega Man being in Smash Bros is the fact nobody at Capcom seems to give a sh!t about the series anymore. The only reason Snake got in is because his creator, Hideo Kojima is Konami's top designer and he wanted him in and worked out a deal to get him in. Since the creator of Mega Man has now left Capcom, there's nobody with any real power at Capcom that probably even cares if Mega Man gets in and would be willing to try and work a deal out to get him in.
The only way Mega Man can get in is if he becomes the most requested character for the next Smash Bros like Sonic became for Brawl, which makes Nintendo actually go over to Capcom to asked for their permission to get Mega Man, like they did with Sega for Brawl. The problem with that is the Mega Man franchise has never been anywhere close to the popularity as Sonic. Plus there's been so many different Mega Man series by now, all the different Mega Men will end up splitting the votes, which will make sure none of them come any where close to the top of any list.
If there's a Capcom character that gets in the next Smash Bros, it'll probably be a Street Fighter character since the guy who's currently in charge of Street Fighter, Yoshinori Ono, has stated he'd like to have a vs Nintendo crossover and that he'd like to talk to Sakurai about it. Then when this news started causing rumors to get out of hand, Ono went and apoligized to Iwata himself. So we have the guy in charge of Street Fighter, saying he'd like to contact Sakurai, and has had some contact with Iwata which he says was to apologize. I'd bet good money that Ono has contacted Sakurai and that they've worked out a deal to get Street Fighter character to be a guest star in the next Smash Bros. This might explain why even Nintendo themselves hyped up Street Fighter IV for the 3DS, more then any other third party title. Plus I bet the Cafe will probably get a port of Street Fighter IV: Arcade Edition and Street Fighter X Tekken as well.
So yeah, right now my money is on a Street Fighter character being playable in the next Smash Bros. Which will hopefully allow for Ono to actually do a Nintendo vs Capcom game in the future because of it.