Katie Linendoll, in an interview with Mr. Miyamoto about Super Mario Run and other behind-the-scenes discussions, asked about other characters Mr. Miyamoto had worked with that never became quite as popular as he had hoped. Mr. Miyamoto jumped to Fox McCloud from Star Fox, and also Pikmen. He said he will have to put more effort into those series to correct this.
So there you go! Once again, Nintendo is not, and never has been, in the business of killing of franchises, even if they don't work out as well as expected. In fact, it looks as if Mr. Miyamoto will put even more time into Star Fox in the coming few years. With luck and "energy", I think he can find some magic that is both new and even more successful than the series' current high-water-mark: Star Fox 64.