Nintendo wouldn't do a thing with Mega Man. Quite frankly, they don't care about him anymore either.
In other words, Rare's situation would basically repeat itself.
Don't jump to conclusions. Let's see the main reasons contributing to Rare's loss:
- A lot of the original staff had left
- Nintendo owned around 49% of the stock, didn't renew it
- Sold to Microsoft to ease investment losses
- Mark of quality was starting to decline (e.g., StarFox Adventures)
What do we got with Capcom? Many consider Capcom to be a shadow of it's former-self. They've made some very questionable business tactics (on-disc DLC, milking franchises, creating franchise sales plan to warrant sequels). Some of their more recent games have had their original essence watered down to a point of providing horrendously-boring experience devoid of original gameplay (RE5-6) or alienating fans (DmC). The only thing they've done right so far is how they've handled Monster Hunter.
Why does the prospect of Nintendo buying Mega Man (or even Capcom) such a highly-lauded idea? There was a huge string of cancelled Mega Man projects revealed from this decade, the most critical of which being Mega Man Legends 3. The only official titles we've gotten thereafter were a couple of bad mobile games and a retooled fan project (Mega Man x Street Fighter). Sure, we have spiritual succesors like Mighty No. 9 and Azure Striker Gunvolt now. As much as I support those titles, they only cement the bittersweet limbo of the possibility of getting a true Mega Man sequel.
Even Keiji Inafune said that he would like Capcom to develop Mighty No. 9 as a Mega Man game.
The only way Mega Man's legacy has managed to remain accessible these past two generations is through rerelease. Most of Mega Man's games were focused on Nintendo systems, so they're the easiest to emulate for the VC. Not to mention we recently got Mega Man Battle Network and Mega Man Zero back with the advent of GBA and DS VC on the Wii U. Today's the birthday of Mega Man, so Nintendo is putting an even bigger sale for the franchise in commemoration than they have ever before. And the icing on the cake of their treatment? Mega Man's decade-long hiatus ending with Super Smash Bros. 4!
tl;dr Nintendo's been the only company to keep Mega Man's interest alive and it's very stupid it's taking this long for Capcom to capitalize on it by making new games.