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I'm not a comic reader so I'm not really familiar with a lot of characters, but here would be my list for the villain side:
Darkseid Metallo Count Vertigo: His ability to throw melee fighters off-balance and disrupt the aim of projectile fighters could work well in a fighting game. Bronze Tiger: Seems like a perfect fit for a fighting game (may be his likeness to King from Tekken). He's going to be on this season of Arrow too. Giganta: Being able to increase in size could work well in a fighter (both as a character power and as a super). Bizarro: Designed to play exactly opposite of Superman!