Mewtwo shouldn't be THAT hard to make.
All they hafta do is animate him, give him hit sparks, give him a voice actor, and balance him. Though to be honest, I didn't consider custom move sets.
and reguarding "2D fighters being easier than 3D fighters"
HOOPLAAAAA!
Characters in Injustice, Killer Instinct, and Marvel had more "holy crap" animations and cinematic in their game play. They also had complete combo systems, more moves attacks and animations, unique artwork and voice acting. and special interactions with the rest of the roster.
Playstation Allstars had 3 times the moves smash characters did and had the "super" animations, as well as 3 alternate costumes per character with 4 different colors each. They all also had cutscenes.
Skull girls is a 2D sprite game... Fun fact 2D sprite games are way harder to make than 3D model games. and wanna know something worse? Skull Girls is completely hand drawn!
Last thing I want to point out. You mentioned balancing and being able to zoom in and look at characters. That isn't major... All of these games did similar things too. so that argument is irrelevant.
@mael a down side to the pokemon trainer is not only the stamina thing, but Squirtle, Charizard and Ivysaur all had weaknesses from their games.
Squirtle took additional damage from Electric Attacks, Ivysaur Fire, Charizard Water, ect.