So if Captain "no powers" America can fight, Iron "superstrong" Man, why is Aqua "Stronger than Captain America"man vs Super"bit stronger than Iron Man"man any harder to believe?

So lets look at it this way, if you say Iron Man vs Cap is fine, then how about, Hulk vs Night Thrasher?
Or Thor vs Jubilee?

Wheres the balance there?

Each company has got a wide spectrum over lesser powered and over powered characters.
Marvel does not have the better balance by a long shot!

Fer fucksake, we have seen some great DC battles over the years that would not make sense by your definition (Batman vs Supes, Aquaman vs Wonder Woman etc)

And anyway, this game is MK vs DCU, not DCU vs DCU!