One my biggest beefs with Nintendo is that in the Iwata era there is an overdependence on franchises and a lack of variety. Next Level Games has no identity. They're just a team that gets handed existing Nintendo IP. If they didn't make Luigi's Mansion 2, someone else would have. Retro proved to be brilliant with Metroid Prime and are certainly given a little more freedom than Next Level. But still, all they make are games using existing Nintendo IP.
I don't see much point in investing in additional devs if they're just going to make the same stuff EAD would make. Back when Nintendo had Rare it wasn't just DKC games. Rare made original IP that had a distinct identity. A Rare game was different from a Nintendo game. You could tell and they would do things Nintendo wouldn't do and introduce characters and IP that Nintendo would never make. Nintendo themselves would never have made Perfect Dark themselves in a million years. Not only was it an IP EAD would never make, it was in a genre they would never bother with. During Silicon Knights brief time with Nintendo they started working on Eternal Darkness in the Yamauchi era, an original IP which is, again, totally unlike anything EAD would make themselves. During the Iwata era they were used to port Metal Gear Solid.
Maybe Nintendo doesn't want their devs to have unique identities so that they don't get bought by Microsoft and can be easily replaced. I get that idea but they might as well be EA or Activision with a better track record if they're going to do that.