In terms of the film Fox was likely to make, nothing of value was likely lost.
But I'd be surprised if Disney isn't at least looking at establishing some kind of licensing deal with Capcom. Mega Man is a non-Disney series that would fit perfectly as a Disney or Marvel-made film. Hell, Capcom has more than a few such series on their belt, and also other series for diversity that could make great films in the hands of the right director. The two companies are not strangers to each other by any stretch, and Capcom is not interested in nor does it have the resources to make big-budget films, so it's not exactly competition, either. Mega Man has the right ingredients to become a box office mega-hit (pun intended) and Disney has the resources to make it into one.
I do think a live-action Mega Man film could work, but it would involve making basically all of the robots CGI characters. But Disney probably would just make it a pure CGI film, unless they were planning to make a Capcom cinematic universe or something, which is unlikely at best, since they'd need another visionary like Kevin Feige to handle it (though I could see Feige being a supporting visionary on such a project, if he's interested enough, the guy might be at least tangentially aware of Capcom's stuff via the Marvel Vs. Capcom series).
