If they really absolutely have to keep an annoying environmental hazard in the Metroid stage, they could do Sanctuary Fortress from Echoes. Have it occasionally warp into Dark Aether, and if you aren't inside a light bubble, your damage slowly rises.
We'll probably get Other M's Bottle Ship instead :lol
Here are some bad ideas
Artifact Temple - Metroid Prime: Neutral floating stage set above and away from Prime's artifact temple. Meta Ridley does battle with Chozo Ghosts in the background.
Sanctuary Fortress - Metroid Prime 2: Basically Kevin Cow's idea. Set in the elevator shaft where Dark Samus is encountered. When the elevator reaches the top of the tower, it runs into a dark world portal and remains that way for a period of time, at which point the elevator falls to the bottom of the shaft and back into the light world.
Patch Land - Kirby's Epic Yarn: Lots of unexpected hazards that play with environment. A hazard may come out of a zipper that runs along the floor, for instance.
Sunset Shores - Donkey Kong Country Returns: Full on silhouette level. Tiki pirate ships will occasionally fire at the stage similar to the cannonball stage from World 2.
Bramble Scramble - Donkey Kong Country 2: Brambles will dynamically grow, twist, and contort around the floating stage, opening and closing angles at which to launch your opponent off. Massive damage is incurred by touching the spikes.
Gangplank Galleon - Donkey Kong Country: Neutral pirate ship stage that floats around both DK Island and Crocodile Isle. Kickass music with awesome stuff in the background.
Dr. Wily's Castle - Mega Man 2: Avoid hostile robots and occasional Mech Dragon attacks that force the stage to scroll further and further to the right...all while *that* song plays. Face off with one of Dr. Wily's huge machines when the stage reaches it's endpoint, before everything resets.
Gusty Garden Galaxy - Super Mario Galaxy: Large space that contains multiple spherical planetoids with their own gravity. It's like Hyrule Temple on all sorts of drugs.