Looking at your vast roster, I'd take a sidescrolling beat 'em up with the Arkham aesthetic, the Guardian Heroes approach to enemies/NPC's and vast rosters (and Vs mode where no character is too underdeveloped or too ridiculous to play as), and the relatively straight forward, kick ass simplicity of something like Tekken 3's Force Mode.
That way we're not just getting too much of Netherealms formula or taking away from what Injustice is already doing to try and produce an EVO level moveset for Commissioner Gordon and Alfred, but they can still come through.