Namco-Bandai is developing Metroid Prime 4?

[A Black Falcon]

Well, they did a lot of the coding for the latest Smash Bros, but the design still seemed to be handled by Sora.

Yeah, there they just did the programming, Nintendo / Sora did the design. This is, it seems, different, and an actual Namco-developed game. And that's the problem, while they can be a fine developer I definitely don't trust them to get Metroid Prime right! They'll need to prove themselves on this one, I'll only believe it'll live up to the greatness of its predecessors if it actually happens.

I know a lot of the original Prime team left Retro for the greener pastures of... Recore? (Wait Recore? Is this right? Oh... oh that's disappointing.)

It is true that Retro has lost a bunch of the staff who made the Prime games, but even so I'd trust them more with this one than Namco...

The problem is, will the story actually be any good at all, or will it get directed by people who still don't "get" the character and who will make the story as per Japanese modern anime trope checklist?

Yeah, this is something to definitely worry about. At this point I'd be more surprised if it DIDN'T have that kind of stuff in it than if it did, which is pretty sad considering what kind of game Prime is.