Bimbo mode
Higher heels, visible zero suit body when you look down with fanart tier proportions, and you can't fight the enemies just rape you
QUICK! Pitch NEW powerups for Samus in the new Metroid!
Anti-gravity boots, allows Samus to run up walls and ceilings.
Beam diffusion. Imbue your missiles and bombs with beam properties. Charge up your plasma beam and store it to make your next X number of missiles plasma missiles that will pierce enemy armor or even explode but still pass through weaker enemies. Make wave bombs to drop through the floor to hit switches that are out of reach. Or maybe even give beam properties to your suit as a whole and run through walls, freeze foes on contact, et cetera. Maybe just guided missiles too? Remote bombs?
detachable psychic breasts
her breasts can now be detached from her body and she controls them with her mind, flying towards enemies and shooting them with psychic blasts or hitting them physically
this will also be key to solving some puzzles as there will be areas that are only big enough to fit her breasts she'll need to have them in separate locations to activate shit
Metroid powers seem pretty obvious. Late game flight allowing for combined use with the speedbooster to do crazy aerial acrobatics could be fun. Bringing Prime 3's grapple energy siphon to 2D is also fine. Maybe push the Fusion Suit all the way now that its latest revision looks really organic. Give us temporary duplication powers to have two Samuses. How about the ability to spawn Metroids? She's the last Metroid as it is. Maybe she should become the new queen.
Samus gets a new "beam" that essentially turns the end of her arm cannon into a drill. With concentrated energy that whirls, she can dig into dynamically destructible terrain.
Give her a green suit that lets her traverse poisonous gases or something
a snaker weapon that will remain in contact with the surface as it travels in one direction
might be useful for hitting things that exist underneath your current platform
ricochet beam, that shouldn't be inobvious and it's just like the r-type bouncing laser or super mario land projectile
just a couple of many ideas
Double Arm Canon.
Or maybe just double Grapple Beam.
Size alteration ray to change item and enemy sizes for physics stuff.