To a point you might be right. Not that Retro would be shut down or anything but maybe this is it for Prime if it doesn't sell well.
There is probably an interview out there that would contradict me but I always thought Other M was Nintendo's reaction to Prime's sales. Unfortunately or fortunately so it sold less than any of the main Prime titles so here we are again for another go.
If this doesn't hit the way that they want you can bet Samus's next 3D outing will be in the 3rd person. There could be a world where 2D Metroid exists, FPA Metroid exists and 3rd Person Metroid exists. I seriously doubt the likelihood of that world though. Or at the very least we do get all 3 but 1st person Metroid is a little more rare with its releases.
I personally can't wait for Other M's 3rd person style to get it's redemption. Hopefully it aint a 3D Donkey Kong kind of wait.