So according to Imran Kahn https://twitter.com/imranzomg the Senior Editor of GameInformer it was Retro who made their pitch/demo for MP4 and Nintendo liked it.
Original MP4 development was very splintered. Different contries made different parts of the game. And ofc some lied about their progress ("Everything is going fine") which lead to a dumpster fire in the end.
He also said that Nintendo is sitting on a completed Metroid Prime Trilogy for Switch but have not announced it for release yet.