1.) Enough with the Batman characters, already! I know he's (arguably) the most popular DC hero, but stuffing the roster with him and his allies/enemies means no room for other characters, and no one will have a chance to learn about, say, Green Lantern, and become interested in his mythos again.
2.) More Magic characters on roster. Considering what's going on with science/tech heroes in recent movies (Dark Knight Trilogy, Man of Steel, Green Lantern) and TV (Arrow, the possible Blue Beetle show), I think Injustice can take this opportunity to make DC's magic-based characters more prevalent in the current fandom (Jonah Hex doesn't count). Wonder Woman and Grundy aside, we could have Zatanna unleash different effects (like slowing, health theft, or summoning) with her spell casting, or (what I REALLY want) have Raven unleash the visage of her demonic father Trigon upon her unsuspecting foes! Hell, let's see how The Spectre, God's Right Hand of Vengeance, would work as a boss character!
3.) How about a joke character? Like, an obscure DC character who isn't canon to the game's story mode, and is unlocked under certain conditions? Plastic Man is the first that comes to mind, but what about Ambush Bug or Creeper? Perhaps a purposefully-weak character that could be Injustice's version of Dan Hibiki?
Since movie Hawkeye and Black Widow are both with SHIELD (currently) how about a solo SHIELD movie separate from the events of the Avengers or leading to the Sequel? I hear AIM is going to be introduced in Iron Man 3, so how about them as the main villains? Or ZODIAC?