Ok, let's go.
Mario: Paper Mario - His moveset would be totally unique, and the Paper series deserves some love
Donkey Kong: Dixie Kong - The helicopter hair offers unique move potential and she's just cool
Zelda: King of Red Lions Vaati - Kind of overlooked villain and he could work as a magic user for a bit of variety
Pokemon: Totodile - Though what I really mean is Gen 2 Pokemon Trainer with Totodile, Bayleef, and Typhlosion
Metroid: Gandrayda - Obscure, but who else besides Samus isn't? Gandrayda could have a moveset based around copying moves from opponents, kind of like an edgy version of Kirby
Fire Emblem: Anyone as long as they're a swordsman Lyn - She's an anime swordsman, sure, but Lyn is cool and she was one of the leads of the first Fire Emblem I played so I like her
Starfox: Krystal - Obvious choice, but give her a staff and base her on Adventures more than Assault and Command and you've got another unique fighter
Kirby: Kirby's True Form Adeleine - The whole paintbrush thing could be unique, but I honestly don't know enough about Kirby to have any real thoughts on how
Earthbound/Mother: Poo - Because his ****ing name is
Poo
Kid Icarus: Medusa - Because she's a babe

Street Fighter: Chun Li - We've got Ryu and Ken, Chun Li is the next in line as far as I'm concerned
Castlevania: Alucard Sonia Belmont - Let's be less predictable and go with the female vampire hunter from that Gameboy game I think isn't canon anymore
Animal Crossing: A Gyroid Tortimer - Because why not throw an old tortoise into the mix?
Yoshi: Kamek - I don't know, wouldn't any character count as a Mario one, technically? I think Kamek was in the Yoshi games so let's go with that geezer
F-Zero: Dai San Gen - A total WTF choice that would confuse and amuse in equal measure
Metal Gear: Liquid - Because Raiden is crap and Liquid has the best voice in the series
Sonic: Big the Cat Knuckles - He's cooler than Tails and has big fists for a fighting game
Pikmin: The President of the Freight Company - Make him get his hands dirty for once, the freeloader
Mega Man: Dr Wily - Put him in one of his little floating golf carts and maybe he'd be something different to what else is on offer
Punch Out: Mike Tyson - Make it happen, Nintendo
Xenoblade: Lol, literally who cares? Pyra - Honestly, every character in this series is a blur of Japanese genericism so put anyone in, no one will care
Final Fantasy: Tifa - Because I've heard of her
Wario Ware: Ashley - Because she's cute
Bayonetta: Jeanne - Seems appropriate
Splatoon: Callie and/or Marie - Make them a pallet swap, make them a tag team that uses music to beat people to death, just have fun with them
Persona: I don't play JRPGs Morgana - Because he's not a generic anime human
Dragon Quest: Roxy - Because I don't care, I just want to look at pretty anime babes
Fatal Fury: Mai Shiranui - Because see above
Banjo Kazooie: Bottles - Just imagine it, ahaha, he'd be useless