I kinda agree. All your ideas are cool, but if anything, Nintendo should go to Metroid's roots. It was first created taking a lot of inspiration from the Alien franchise. Why not taking the Alien formula again but this time from Alien: Isolation? That would be the kind of game you are referring to.
Now, talking about NPC's... one of the most important elements of this franchise is the isolation feeling. So the less NPC there are, the better. Audiologs? I'm on board with that.
Now, Mother Brain, she/it is supposed to be a Super Artificial Inteligence, but a Glados like character? No, just no. Again, Mother Brain takes elements from MU-TH-UR from the first Alien movie. You are not supposed to hate it because it doesn't display any feelings.
