Frankly I think Kratos even without any fancy plot-powered weapons can defeat ganondorf. He may not technically succeed due to not permanently killing Ganondorf but he can still defeat him.
Link due to his character will deny serving Ares who will then proceed to break his spine in half and setting him on fire by looking at him. He probably won't save the captain which will mean he won't get out of hades and he probably will refuse to complete the challenge of pandoras temple that involves sacrificing an athenian soldier, and assuming he gets past this somehow link lacks the physical strength to overpower Ares who could match a 300 foot tall Kratos.
Both of them are screwed.