Why not, though?
From Nintendo's perspective:
- The Mighty No. 9, while coming from a proven director and figure of the gaming industry, is not necessarily a sure-seller. It will have immediate pull among fans that recognize the Mega Man brand, but I think we all can see that Nintendo requires more than just the hardcore support for the Wii U.
- Going back to the prevoius item, Nintendo heavily depends on third parties giving them the time of day. Although they may have landed themselves a deal with Capcom for both Monster Hunter 4 on 3DS, as well as a cameo appearance for Mega Man in Smash Bros., a continued partnership is absolutely necessary to ensure that they are not the only ones supplying games to the Wii U.
- Having Nintendo maintain a policy in which the Mighty No. 9 does not appear on Nintendo systems is a quiet, non-obvious way for Capcom to get 'even' without outright calling for a cease-and-desist measure against the project. This doesn't blockade the game getting greenlit on the other two systems, but it's, again, a way for them to essentially stop it in petty ways without having a large, publicly available spread of effect.
Just some thoughts. Would it effect the sales of Mighty No. 9? Not in the slightest - the prime platform here is PC.
Would it affect the sales of Smash Bros? No, of course not, and I didn't insinuate that in my original post.
The thought here is wondering if Capcom will take a 'lower', quieter method of retaliation to signal to Inafune that they are less than impressed.
Edit: Regardless, backed. I love Mega Man and look forward to his non-return.