Mario: Geno, Waluigi, Captain Toad (if Geno doesn't count due to being owned by Square-Enix, then Fawful)
Donkey Kong: Dixie, Cranky, Funky
Zelda: Midna, Skull Kid, Impa
Metroid: Sylux, Rundas, Zeta Metroid
Yoshi: Kamek, Baby Bros., Baby Bowser
Kirby: Bandanna Waddle Dee, Dark Matter (his swordsman form from Dream Land 2), Adeline and Ribbon (not sure about including Marx since he's a boss)
Star Fox: Krystal, Peppy, Andross (based on his model from Star Fox Zero, which gives him a body)
Pokemon: Genesect, Rillaboom, Mimikyu (not overly familiar with Pokemon beyond Gen 3, so there are probably better choices)
Earthbound: Giygas (Mother 1), Porky (Earthbound), Masked Man
F-Zero: Black Shadow, Jody Summer, Zoda
Fire Emblem: Edelgard, Ryoma, Tiki (to be honest, not overly familiar with Fire Emblem outside of a handful of games)
Kid Icarus: Medusa, Hades, Phosphora
Wario: Captain Syrup, 9 Volt, Jimmy T.
Pikmin: Alph (as his own character), Louie, Plasm Wraith
Animal Crossing: Tom Nook, Tortimer, Mr. Resetti
Punch-Out: Doc Louis, Mr. Sandman, Glass Joe
Xenoblade: Elma, Rex/Pyra/Mythra, Fiora
Splatoon: Octoling/Agent 8, Squid Sisters, DJ Octavio