I admit I haven't tried Other M based mostly on GAF dislike, I'm always pushing it in my Wii backlog. I don't have anything after Rhythm Heaven as I imported Xenoblade so maybe I'll search for it.
The story is the only weak part of Other M. The gameplay and controls are spot on, well minus the sections where you have to find something looking in FP mode. It controls super smoothly and by the end of the game you're dodging, shooting, and killing things like you would expect Samus to.
They tried to experiment a bit with how you go about acquiring items through out the game. So instead of an explosion knocking out half her suit, you have her agreeing to work with the GF forces, which means she has a commanding officer and has to listen to him as to what she can and can't use on this ship.
It's very much an evolution of what was done in Fusion, and folks saying otherwise are just sticking their heads in the sand going lalalalalalala. If you play Fusion, and then play Other M, the similarities and evolution of ideas becomes blatantly obvious.
I personally would love another Metroid game using the Other M engine. Just get rid of the hand holding seen in Other M and Fusion, take out the FP mode (for missile use and looking for something) and put Samus on a planet again. I would love to see "Metroid Dread" finally come out say for the 3DS using the Other M engine.
This is coming from some one who has loved the Metroid series since the NES one. Don't listen to the hyperbole, and play the game.
That said, as much as I love, love, love the Prime series, I want Retro making something different for their first Wii-U game. They seem to do 2 games a generation, so let them make something different first, and then a new MP. Give them a break from the Metroid world so they can refresh, and develop new skills and come back to it even stronger.
As I've said many many many times on this board I really want to see Retro do Star Tropics for the Wii-U. They have an amazing skill and talent at creating believable worlds. I think they would do a better job with that, then them handling something like Zelda. I think they would be wasted on doing a racing game like F-Zero.