I think Zod was not made for "physical" fights, he was born as strategic leader of an Army.
Faora was made to be a "super soldier" with great combat skills and low emotional abilities.
So that feelings like mercy or moral aspects are not able to soften her up. They did this genetic change to make sure, that Faora will follow her orders, even if she has to do a genocid.
Kal-El is free born - that does not necessarily mean, he is weaker in combat. He is just free. He was coincidentally quite muscular - i think that helped him alot versus Zod.
Thanks for clearing that up Niko176; that makes much more sense.