The worst argument by far though is where you basically admit that Nintendo doesn't need Metroid Prime 4, but then are skeptical of Retro's ability to deliver just because of the past 5 years. That might not seem like a contradiction, but think about what's being implied there. Metroid Prime 4 was never a title Nintendo "needed" to do, Metroid isn't a big console seller. If Nintendo didn't have legitimate faith in Retro, they would have just cancelled the project outright. Even in early 2019, they never needed Metroid Prime 4 because the Switch already justified it's existence with a laundry list of high quality exclusives that, unlike Metroid, actually sold a significant amount of systems. So why would the game even be entrusted to Retro unless they had the actual capability to deliver?
Metroid isn't a very important IP in terms of attracting a wide audience; the core Nintendo fanbase are not very big fans of those types of games. It is an important IP to certain very loud fans. If Nintendo outright cancelled it, they would get incredibly bad PR by those very loud fans. Similarly, Retro is a highly overrated studio by mostly the exact same loud-Metroid fans. If Nintendo shut down Retro without proper justification, they would get similarly poor press from those loud fans.
A win-win situation is to give Retro Metroid Prime 4, see them fail with it, and then close the studio with little to no backlash. Also, top brass are not the people who created the game, they're the people that managed its production - and from what I heard of the original Metroid Prime games, it was a fairly horrendous production.
None of the Metroid Prime 2002 design team remains with Retro. None of the lead or senior artists or engineers are with Retro (or Nintendo). Six Retro studio artists and engineers (none of them leads or senior staff in the Metroid Prime era) were onboard with Retro for DKC Tropical Freeze. There are many times more former Retro devs (from the MP era) in Armature Studio (https://www.mobygames.com/company/armature-studio) than there are in Retro, and the ones there played far bigger roles in the development of Metroid Prime than anyone currently in the studio; since it is a studio containing the majority of the senior staff from the Metroid Prime dev team, while Retro currently has none of the senior staff.
You can look up their bios here: https://www.mobygames.com/game/gamecube/metroid-prime/credits
If Nintendo really wanted to give the game to the studio most familiar with Metroid Prime, they'd go out of their way to get Armature Studio to do it.
I know you don't want this to be true because you're a fan (and I admit, I'm not), but you have to question Nintendo's motivations for putting the game in Retro's hands when they clearly don't have the staff for a high-end FPS on the Switch.
I describe myself as a little dose of toxic masculinity.