I will say I think the pitfall with judging a Nintendo vs Capcom roster, especially from the perspective of a Smash fan
I figured I should back this up with generally how I might think the Nintendo side could look, so here's a rough draft. As a disclaimer I don't wanna continue to distract from the actual Smash discussion here, and I think we should open up / revitalize a thread with this concept, but just before we're totally past it.
Mario, Luigi, Peach, Bowser, Donkey Kong
Link, Ganondorf, Samus, Kirby,
Tom Nook, Inkling (Agent 3)
Chrom,
Tiki, Olimar, Captain Falcon, Fox, Little Mac,
Saki, Lip
DLC: Wario,
Tetra, Ridley, King Dedede, Shulk
It's roughly the size of MVC3 base. Admittedly, this still doesn't feel like it goes quite far enough. A couple obscure Nintendo picks, a more eccentric Fire Emblem pick in Tiki, a different form of Zelda to shake things up. Tom Nook stands in as the Animal Crossing character this time, and Inkling might be tackled with a slightly different angle in mind. I contemplated Squid Sisters but MvC doesn't quite do duos, or stance characters like Smash since it's a team based fighter. It does showcase how difficult it is to detach yourself from Smash, and also how many cool things have to be absent when condensing Nintendo.
DLC does play into some more Smash-familiar faces, but I think the different gameplay style would let them shine in a new way. Ridley and Dedede are a bit self serving but I think they feel ripe for exploring here. Shulk is by default the move for Xenoblade but maybe they can go a little crazier.
I left off Pokemon, because quite frankly that feels like its own beast. I'd have loved Mewtwo in a game like this but I think Smash is lucky that it's allowed to use Pokemon in the first place. Negotiations as well as catering to Pokemon Co's demands might be more work than it's worth starting from scratch. It would also make it virtually impossible to fit in the weirder picks because you'd have to dedicate like three slots to Pokemon alone.