Retro likely isn't working on Metroid Prime. The team isn't there, it's not fit to create an atmospheric first person adventure game.
My guess is that they are currently working on a new I.P.
Right, but they still did a good job on Tropical Freeze, no? I know a 2D platformer is not the same as a 3D first-person shooter/adventure game, but quality is quality.
They did a fantastic job with Tropical Freeze. It's one of the best platformers ever made. However, it's like asking the worlds best pancake maker to make a burger. It isn't going to happen just yet.
A couple of years down the line, could retro be fit enough to make a Metroid game? Of course. But instead of going to A to Z, they will likely do something in the middle. Perhaps something like an RPG, or a 3rd Person Action-Adventure game.