Shinnok should be able to defeat Shao Kahn without too much trouble due to his superior magical abilities. Furthermore, Shinnok has had all of this power and knowledge for millions and millions of years. If that isn't a long time, then I don't know what is. So that should give a clue as to who has (and had) more experience with regards to using magical powers. Obviously, the more experienced the combatant is, the more skilled he/she will be. Shao Kahn's knowledge is mostly confined to the black arts, and this knowledge is minute compared to the knowledge that Shinnok has. While Shao Kahn is well-known for his arrogance and overconfidence, Shinnok is most well-known for his wisdom and cunning. So this should also give a clue as to why Shinnok has the advantage here. Besides, Shinnok should always be beyond what Shao Kahn is or could ever be because of his "Fallen Elder God" status. Shao Kahn's superior physical abilities (strength and such) won't really matter.
@lagoon_boy: You do realize humans cannot move fast in or underwater. I am a scuba diver and this is fact. Batman may give Jaws a couple of battle scars from the knife and batarang, but he is getting eaten here
Since this is gonna happen eventually in games Ill get the debate started. Cole is his Infamous 2 incarnation with the Amp and Ryu and Ken are both th their most powerful (Street Fighter 4 incarnations). Fight takes place in an abandoned New York City and Morals are on. Fight goes until one side is either KO or dead.