There are other factors involved as to why the Mega Man franchise is in it's current state of hybernation, most of them having to do with Inafune's departure and the company restructuring. I don't think the sales of MM9 and 10 were a factor at all.
The main problem is that the series doesn't put up big figures, and it really hasn't been since probably the Battle Network series, and even then, those were good sales for a lower budget game, but with the budgets and expectations of todays games, it might not work.
One could argue that Capcom could fund some smaller, but high budget 2d games and rely on smaller but reliable sales as a way of profiting, but I don't think the company is interested in focusing on small time sales that chip away small profits, and instead huge figure games (RE, SF, etc). I guess you could say the industry has kind of outgrown Mega Man. A game that sold 500k or 1 million before would be considered a success of some sort and worth investing in, but nowadays that seems to be considered a failing figure for larger budget games.
I don't disagree there are political and company structure reasons the series is being neglected entirely, but it's also obvious if the games sold a lot, they would continue to make them. I think we as gamers think a company should be happy if they spend 10 million and profit 20 million, but most companies seem to need to make far higher profit margins and unfortunately chase bigger money even to their own doom (RE6, Dragons dogma, DMC).
By no means do I think Capcom is doing the right thing, they went from being one of my favorite companies to being almost useless now, but the loss of MM is something I can't really say they are stupid for, as i'm not even sure how to approach making that series big again while not pissing all over the fans who love him.
I retract that Mega Man 10 sold 'abysmal' and was over stating, but all signs point that it was a significant drop from 9 and not something worth pursuing further, meanwhile, COD games keep selling the same or more each year, as does creed, Madden, and basically any other sequel to other games. I really think the only way the MM series could become a 3-5 million seller is if Nintendo owned the IP and put their big time people behind it, and even that would be a challenge they might not be up to.
Fans have all the right to be upset (as I am) but they should also point the finger at the people who do not support the series in general as the fault, otherwise we would have had Powered up 2, Mega Man 11, and a sequel to Legends and Advent. Money talks, and fans failed to put up the money regardless of what system the games released on, with plenty of excuses to go around (too many sequels, not interested in this style of Mega Man, don't own that system, etc)