Right, I'll actually reply to this post with something worthwhile.
I thnk that Batman was paired up with Sub-Zero because they are the main anti-heroes of each franchise. Although he would be cool against Kano, he could probably tackle the whole of the Black Dragon. Bring them all down.
The only one I could think of being a good match for Superman depends on the outcome of Armageddon. If we are assuming that Konquest was canon and Taven became a full god and Edenia's protector, I think he might fit the bill, as he is much younger and probably more able-bodied than Raiden or Fujin. Shinnok would make a decent Superman enemy, being a fallen Elder God and all. But he'd need his full power returned to him.
Scorpion would have to go against another undead, like Solomon Grundy or Deadman. Being neutral, he could take either.
And we haven't seen any other characters but there are some match ups, Havik and Lobo, Shang Tsung and Dr. Fate, Wonder Woman and probably Sindel, because of the flying, Reptile and Killer Croc, I dunno. there's more.