I'm not bringing in just games, I'm talking about the incarnation that the characters are most famous for. In this case, we have comic book Flash against video game Shao Kahn. If we wanted to argue that Kahn is more powerful in a different universe then in the Batman thread you open up people to using this against Batman.
See how awful of a point that can be? Shao Kahn is known for his role in a video game. Flash is known for being a comic book superhero. You can't get movie Kahn where he only kicks ass for about 45 seconds before being carried away by a dragon.
I would also like to note that a kick from Shang Tsung pushed Kahn a good 5 feet in that cut-scene. That does not hold good water for withstanding a hit from Flash.
Are you seriously bringing in that shit Mortal Kombat vs DC game to help your point? They stated numerous times they had to tone down the DC hero's in order to balance them against the Mortal Kombat combatants. I could easily replay that garbage game and have Flash win that fight, regardless of how toned down they had to make the DC fighters. The fact that in this video game they had to tone down guys like Flash to put him on par with Kahn further proves the point Flash should be winning this fight hands down.