The situation becomes way less confusing when one remembers Miyamoto's personal motto:
"
New ways to play".
It's practically become the entire company's MO because organizational ideology is a really strong force (especially with long-lasting organizations, but also with younger organizations) and those at the top - like Miyamoto - have a lot of influence because they get to have a stronger say over what gets made or whatever. Now, Nintendo's not as set in their ways as say the Catholic Church* is, but it's evident when Miyamoto said to Bill Trinen:
"So maybe if we create a new controller interface, and we find that particularily suited to F-Zero, then maybe we'll do something with it again in the future".
Which... honestly, gets to a main issue I believe Nintendo has. Many within Nintendo, including Miyamoto, get the impression that their games, characters and consoles are so beloved because of the play control they're associated with. Which doesn't take into account that a lot of hardcore Nintendo fans also get attached to Nintendo's characters because of the characteristics. It's kinda the drawback with organizational ideology - the thinking they encourage might lead to a lot of people within the organization not entirely "getting" (for lack of a better term) all aspects of their success / popularity.
*(I bring them up because they've existed for a 1000+ years, some of its quirks have existed relatively unchanged for
centuries because of its organizational ideology. Other corporations like Coca-Cola have also deeply-entrenched organizational ideologies, like not ever revealing its recipe.)