That's a pretty cool idea, I'll give it a shot.
stay.
gets to stay due to having gender differences,
gets to stay thanks to being stereotypically female-coded.
stays but only as Spiky-Eared Pichu.
Mii Fighters stay too I guess.
To that I'd add:
Toadette
Dixie Kong
Midna
Tetra
Toon Zelda
Adeleine
Krystal
Eevee
Gardevoir
Lyn
Mona
Ashley
Captain Syrup
Medusa
Viridi
Brittany
Fiora
Elma
Octoling
Ribbon Girl
Min Min
Twintelle
Dr. Coyle
Amy Rose
Roll
Tron Bonne
Ms. Pac-Man
Chun-Li
Terra Branford
Jeanne
Gruntilda
Mai Shiranui
And from new series:
Akari Hayami (1080°)
Ashley Misuki Robbins (Another Code)
Officer Howard (Astral Chain)
Kissy (Baraduke)
Qucy (BoxBoy)
Bubbles (Clu Clu Land)
Kasumi (Dead or Alive)
Jill (Drill Dozer)
Alexandra Roivas (Eternal Darkness)
Tethi (Ever Oasis)
Ayumi Tachibana (Famicom Detective Club)
Yuri Kozukata (Fatal Frame)
Fossil Fighter
Barbara the Bat (Jam with the Band)
2B (NieR)
Starly (Starfy)
Blaze Fielding (Streets of Rage)
Savvy Stylist (Style Savvy)
Mach Rider
Monster Hunter
Amaterasu (Okami)
Lip (Panel de Pon)
Aya Brea (Parasite Eve)
Joanna Dark (Perfect Dark)
Chell (Portal)
Arle Nadja (Puyo Puyo)
Jill Valentine (Resident Evil)
Ring Fit Adventurer
Shantae
Ivy Valentine (Soul Calibur)
Ulala (Space Channel 5)
Musashi (Sushi Striker)
Lara Croft (Tomb Raider)
Reimu Hakurei (Touhou)
Carmen Sandiego
Disclaimer 1: I don't consider Dark Samus to have a gender, so I don't think it counts, but if it did then by all means keep it.
Disclaimer 2: I interpret Sheik as female, so that's why she's there.
Disclaimer 3: I don't know what NiGHTs is, if I were sure she'd be there.
Disclaimer 4: I expect to have missed characters that will be insultingly obvious to me in retrospect. (Like Reimu!)