A Nintendo Vs. Capcom game would preferably stay away from just regurgitating Smash's roster into a traditionally fighting-game set up and try and work in characters who otherwise won't be playable in Smash anytime soon for a variety of reasons... Admittedly it's hard to stray far away from Smash (or previous Vs. Capcom games) without feeling like you've left major characters out.
Going for 26 characters each side, 52 in total. Not very realistic, but whatever.
Nintendo
Mario (Super Mario Bros.)
Bowser (Super Mario Bros.)
Peach (Super Mario Bros.)
Yoshi (Yoshi's Island)
Wario (Wario Land/Ware)
Cranky Kong (DKC but partially build his moveset around wacky DKArcade references)
Link (The Legend of Zelda)
Zelda (The Legend of Zelda)
Ganon (The Legend of Zelda)
Skull Kid (The Legend of Zelda)
Kirby (Kirby's Dreamland)
Pikachu (Pokemon)
Lucario (Pokemon)
Pokemon Trainer (Pokemon, trainer spawns a different Pokemon for every attack like a streamlined version of the Brawl character)
Fox (Star Fox)
Samus (Metroid)
Ridley (Metroid)
Captain Falcon (F-Zero)
Ness (Mother/Earthbound)
Marth (Fire Emblem)
Pit (Kid Icarus)
Doc Lois (Punch-Out!!)
Isabelle (Animal Crossing)
Wonder Red (The Wonderful 101)
Inkling (Splatoon)
Lip the Fairy (Panel de Pon/Tetris Attack)
Capcom
Mega Man (Mega Man)
Roll (Mega Man)
Dr. Wily (Mega Man)
Zero (Mega Man X)
Sigma (Mega Man X)
Tron Bonne (Mega Man Legends)
Ryu (Street Fighter)
Chun-Li (Street Fighter)
Guile (Street Fighter)
M. Bison/Vega (Street Fighter)
Juri (Street Fighter)
Arthur (Ghouls n' Goblins)
Red Arremer/Firebrand (Ghouls n' Goblins/Gargoyle Quest)
Jill Valentine (Resident Evil, give Jill her MvsC2 moveset which spawned different classic RE enemies)
Leon Kennedy (Resident Evil)
Viewtiful Joe (Viewtiful Joe)
Amaterasu (Okami)
Nina (Breath of Fire)
Some monster hunter fuck I don’t know
Mike Haggar (Final Fight)
Phoenix Wright (Phoenix Wright)
Bionic Commando (Bionic Command)
Sissel (Ghost Trick)
Zack & Wiki (Zack & Wiki)
Vanessa Z. Schneider (P.N.03)
Captain Commando (Captain Commando)
Another all star Nintendo fighting game is redundant. Wake me up when Mortal Kombat vs. Street Fighter becomes a thing.
I don't see how they can reach a decent compromise between having a Mortal Kombat game without fatalities and having the iconic and (somewhat) 'clean' Street Fighter cast getting brutally murdered that doesn't just disappoint everyone.