Copying the Ultimate Ninja Storm series makes the most sense when taking into account moves and abilities the Pokemon have. I hope it's not an NFC game, because then I won't buy it.
Have all 25, non-legendary, fully-evolved fighting Pokemon in the game - include Mega Mewtwo, Cobalion, Terrakion, Virizion, Keldeo, and Pirouette Meloetta as DLC.
I don't see why pre evolutions can't be in the game as well.
A number of them aren't even fighting types - Poliwag, Poliwhirl, Torchic, Shroomish, Ralts, Kirlia, Chimchar, Tepig, Chespin and Quilladin. In the games all Pokemon aren't created equal - I know this game would not be canon - but having a Tyrogue take out a Blaziken would be silly.
I don't think it would be silly at all. The ninja storm series has young characters like kid Naruto and Obito taking out guys like Madara and Hashirama. The same dynamic can happen here.
And with the fighting types, they can take liberties. While Pokemon like Poliwag, Shroomish, and Torchic wouldn't fit, I don't see why Poliwhirl, Kirlia, and Quilladin can't. Same with other guys like Snorlax, Alakazam, and Electivire.
What I want to know is how they'd handle types. They obviously can't do 2x damage, but it'd be tough to justify ignoring typing altogether.