Dude, loved the post.
Although I don't know much about Dark Samus, her stage could be the place where we fight her in Metroid Prime III: Corruption, something like this!
This is the Sanctum in Phaze, a planet made out of Phazon so it's like Dark Samus sort of homeland!
And as for another metroid stage, I would personally like a Tallon overworld one from Metroid Prime: 1
RE: How I Would Reboot Super Smash Bros: Part 7 - Pokémon & Metroid Stages