According to the Internet Movie Database, 12-year old actor Zachary Gordon is reportedly listed to portray Mega Man in Marvel Vs. Capcom 3.
While this is by no means a 100 percent confirmation for the Blue Bomber, it's looking pretty legit as IMDb apparently "lists things as rumored when they haven't been been substantiated," according to Event Hubs.
On the flip side, IMDb isn't perfect -- the site does post inaccurate information on occasion, although a majority of the info on the database is usually correct. If the listing is indeed legitimate, this means a Mega Man incarnation will be a playable character -- an incarnation that requires a somewhat young voice... classic MM, perhaps? A likely choice.
Take this bit with a grain of salt for now; nothing's official until Capcom says so, as usual.
Credit: Event Hubs (Thanks, Amir)