The "Spiritual Successor" as Inufune (seemingly the lead architect of Megaman at this point) being Mighty No. 9, which has almost 4 million dollars loaded into it by pre-sale investitures is already anticipated for release in November of this year for the Wii U.
https://www.kickstarter.com/projects/mightyno9/mighty-no-9 has some information on it, although this site might be outdated due to the productions moving on.
Investors get their picture in the game, a phrase of their choosing, and extra pamphlets and art.
Although I would suppose it's possible that the team could sell the rights to continue production of this genre, that would leave a hefty customer base with contracted Wii U porting in the hands of a different development staff mid-production, which doesn't seem like a likely move to me.
As for the Megaman franchise itself, being that Legends had a 64 port, Megaman X4 on Sony PSX, various arcade appearances like Capcom vs. Marvel, it seems to me that Megaman will probably still be ported to any systems that can currently be utilized to their full potential with the current markets, what's available to which demographic areas, what the people in the development staff currently feel like pursuing, etc. i.e. the way that Megman X 1-4 , 4 being slightly more advanced than the prior releases, made their appearances to me in my area before Megaman 7-9, being a slight step back in graphics and action capabilities being on the SNES but still very fun nonetheless, and especially the obvious difference in lineage being that Wily and Sigma are different characters.
*theoretical cybernetic implanting of Wily's consciousness into the robot known as Sigma maybe?*
Whatever the case, I don't believe that at any time throughout history the developers of these titles are ever going to solidify an exclusive contract for a certain system for the ENTIRE franchise, but deal with those issues on an individual basis, rather.
I mean, realistically, if someone(s) such as the AGN staff or any other people out there made a new hardware/software relationship, be it a handheld, console, arcade, etc., with an easily directed game creation studio, for any reason whatsoever that would seem like a good idea, like power conservation capabilities, faster processors, higher definition sound or video, ideas like that, there would be no real reason to deny the new developers and the Capcom staff the opportunity to do something good for gamers and/or the environment at the same time.