A 2D/3D Metroid could work if they made it similar to DKJB but have Samus just a little bit bigger. She could explore huge lush environments filled with enemies, platforms, gorgeous back drops and giant pedestrian fauna/flora.
As for the story, she is sent to retrieve a very precious super natural type of animal (not Metroids). There are many of them; all of them different, with different abilities. She'd have to track them, find out their weaknesses and trap them, all the while unlocking secrets in the world that will help her progress. She'd start out with all of her abilities (missile/super missile, ice/wave/plasma, bombs, screw attack, spider ball, grapple) but they'd change drastically as she unlocked secrets and traps these creatures. After their capture, they bestow onto her super natural powers, like the ability to miraculously grow thick vegetation, the abilty to project light, and the ability to tame creatures that inhabit the earth. The further she explores and the more creatures she captures, the more powerful she becomes; yet something strange happens. The world becomes more dull; the animals more angry; the sky more dark.....She is killing this world, one by one.