There's also that "Rockman Strategy" game for the PC that was made by a Chinese company, but was still licensed by Capcom. It's really rare, I know of only 3 people in the English-speaking fanbase that possess that game, and the company behind it has since went belly-up.
But any way, tirkaro is really correct with his assessment. Hell, the Japanese care more about Rockman than they do Snake, and especially, Sonic. Those two guys predominantly find their fans amongst the west, but Rockman has always been big in Japan and has a respectable presence worldwide. You might even say that the main reason that Capcom hasn't gone out of business (especially during their rough times back around the turn of the century), was primarily due to Rockman games, especially the highly profitable EXE games on the GBA.
So, I would think that if Sakurai didn't open up the lines of communication months ago, certainly Capcom would themselves, whether or not Inafune was part of the equation or not. There's too much profit to be had for Capcom to just say "no" to free advertising, and only doing more to cater to their homegrown fans, who would like nothing more than to see at least ONE version of the blue bomber in a game like Brawl/X.
Personally, I'm hoping for either the OG or EXE, if it's not such a thing that one could be a costume change for the other. After all, if Network Transmission for the GC is any indicator, EXE is also able to do things like Slide and other classic Rockman conventions. And that's all I could really ask for...