I've always wanted samus to crash land on a planet and be forced in morph ball mode. The entire game would be her exploring and gaining new ball powers and of course at the end she would return to her normal self and escape.
I image the game from a third person perspective, just like ball mode in prime.
The combat would be based around a lock on/strafing style of play with attack moves changing based on the ball powers you gain. I like the idea of a lock on dodging mechanic with quick forward ramming attacks, or a locked on jumping mechanic (with free movement while in the air), then diagonally slamming down into enemies weak spots.
All the metroid staples would work great here, magnetic ball for moving up metallic surfaces, rail riding and puzzles, ice ball for freezing enemies for use as platforms, x-ray ball illuminates area around you showing secrets, enemy weaknesses, good old bombs, power bombs, speed ball (for fast movement during combat, traversal across disintegrating platforms), jump ball, double jump ball, etc. etc.
plus samus's small size could lead to some really cool game play mechanics, like entering a gigantic door locking mechanism and traversing it to unlock the door from the inside. Or being eaten by giant enemies and navigating a moving sort of biological platform puzzle to kill them from the inside (bomb to the brain). It would also lend it's self to stealth (roll from shadow to shadow avoiding enemies she is unable to fight due to size/lack of power)
Plus think of the great corny puns marketing could pretend to avoid "Do you have the balls to help samus face her newest threat" "she has more balls than most men"........
Lastly, there should be no story told by narrative EVER. Exploring the environments should be enough. Features of the environments would imply/tell the story.