Nintendo legend Shigeru Miyamoto, father of Mario and The Legend of Zelda sat down with Glixel and discussed many things, including how Nintendo actually nearly made some like Minecraft.
"I do like Minecraft, but really more from the perspective of the fact that I really feel like that's something we should have made. We had actually done a lot of experiments that were similar to that back in the N64 days and we had some designs that were very similar. It's really impressive to me to see how they've been able to take that idea and turn it into a product."
In a creative sense, if someone other than Mojang created a Minecraft-like game, it seems likely that it would be Nintendo. But what's really interesting are the experiments he spoke of on the Nintendo 64. They're probably very much prototypes, if even that, but getting a public eye on them would be very interesting.
The closest Nintendo has to a Minecraft is probably Super Mario Maker for the Wii U, and recently released for the 3DS. Although, a Minecraft clone today wouldn't so much be called a clone, but part of the genre that Minecraft has created. What sort of game could they make with a Nintendo twist today?