Squall would win. While Cloud is busy worring about whether he's actually who he thinks he is or whining about how much he hates himself because he let some girl die in front of him that he might love but then again he might be responding to his image of the man who saved him who he very well believes to be him which goes back to him wondering if he's actually who he thinks he is...and well you get the idea how messed up in the head he is. Squall would come by, slice his head off and walk away saying "whatever..."
Also, Squall technically has more expierience and training than Cloud does. Squall was raised as a child soldier while Cloud seemed to join Shinra around the age of sixteen. Also Cloud only had basic training. He never got into SOLDIER his abnormal strength comes from the Jenova cells injected into him after the Nibilheim disaster. As for Squall, we don't know how powerful the Junction system makes him. Judging from Laguna's response though, it is inhuman power, so it's safe to say Squall could go blow for blow with Cloud.