Retro's situation is different. Their mystery project was had been in development hell for a while, and they and Nintendo were growing dissatisfied with its progress. At least according to rumors. Next Level is more stable at the moment since they're not an official subsidary of Nintendo, and most of their games under them have gone pretty smoothly.
Plus, Nintendo's not afraid of producing New IP, they're releasing another one in just a few weeks (Astral Chain).
That's a Japanese studio.
The last time a Western studio got to make a major original IP title was ... when?
Nintendo is a very traditionalist Japanese company even by Japanese company standards. Given the cost of modern game development I think they are reticent to give a Western studio a chance at a new IP.
Retro failing every time they've been given a chance at a new IP probably just reinforces the position at Nintendo.