Pete should win b'cos he is more practiced and experienced. During the 5 years (Marvel time) between the original Clone saga and the Clone saga of the 90's Pete was fighting supervillains on an almost daily basis, while Reilly's adventures wre few and far between. Afight between them would be like a boxing match between 2 evenly matched fighters-1 of whome had been very active ( like having 4 Fights in the last 12months) the other of which has not fought for 1year-18 months.
Ben was a perfect clone of Peter with all his memories. So much to the point neither honestly had and real ideal of who the real one was. And they fought to a draw on nearly every occasion that they weren't effected differently by something.
Ben was an awesome character thou. He truly had an incredible concept in his character. Sucks they just killed him off. He had so much still untapped potential. IMO
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Being as how these two fought before, and Reily was locked up in a cooler for over a decade, I'd say Parker could do it once again.... unless Reily is Parker, and Parker is really Reiley.