Not so sure Minecraft would actually be better off under Nintendo than Microsoft.
Depends heavily on how hands off Nintendo is willing to be with Mojang. Microsoft let Mojang continue doing their own thing, including releasing versions of the game on competing platforms. That ubiquity I think is part of the reason why Minecraft has remained relevant for so long. No matter what platform you have, there is a version of Minecraft for you to play, and has for the past decade.
Nintendo, however, has been and still is far less keen on allowing stuff under their mantle on platforms other than their own, let alone competitors. It's possible that under Nintendo, Minecraft would've become less popular in the long term due to exclusive to Nintendo platforms.