It's not meant to be another Prime situation, though, that's kinda the point.

Prime was Nintendo's first attempt to re-imagine the exploration aspects of Metroid in a three-dimensional environment, released alongside a new 2-D game made by the "classic" team that took the game into a more narrative-driven and horror-tinged direction. It was a big push for a franchise that had zero exposure for a long time, it was an enormous gamble, and as we know from the way Retro's story played out, Prime had more than its fair share of bumps along the road.
But Federation Force isn't setting out to do any of that, and it knows it. Just like you said, it's a cooperative, action-focused title that's set in the Metroid universe and borrows some of Prime's control mechanics like the first-person view, aiming setup, lock-on, etc. It's not redefining the genre in any major way (hence why it's not a new IP), and it's not trying to redefine its source material (hence why the "Metroid Prime" part of the logo is comparatively small, and it doesn't even use the iconic screw attack logo like the "main" Metroid games do). It's a game doing its own thing, Nintendo wanted a familiar setting to frame the action in, and Metroid was the closest fit they have amongst their current franchises. Again, it's not that different from how they handle any of their other IPs, but
I guess "because it's Metroid" that makes it a much bigger deal than if this had been a Link's Crossbow Training sequel or a Joy Mech Fight reboot or something. It's a sacred cow mentality that's been mostly removed from any other major Nintendo franchise already.