OK as a nerd, this game hurts my brain and I don't see how it could possibly make any sense.
I mean, there are a lot of powerful characters in the MK universe but effing Superman here! HELLO! SUPERMAN the man who only vulnerable to magic and kryptonite. So unless Kano has magical robot fists or Sonya has kryptonite tits Supes' would be able to wipe the floor with 'em.
Not to mention other characters that could run circles around the MK crew, heck even Zatanna could turn Scorpion into a rabbit before he could say "Get Over Here".
Just... it hurts my brain. At least with Marvel VS Capcom or Capcom VS SNK the pairings made sense (at least until the boss battles).
The very idea of some lamewad like Raiden beating the crap out of Darkseid just... GAH! G-GAH!!
And before someone says "well it's only a game, a alternate universe / fantasy match up" well that's CRAP. You might as well make a game called NHL VS The Care Bears it would make as much sense.
Ok, I could maybe see Mortal Kombat VS The Teen Titans that might actually work because those characters all have limits to their powers, but then you'd have Sheng Tsung getting his ass handed to him by Beast Boy (no actually that still kinda makes sense).