Zack is a naturally gifted Ace who is one of those people who is good at everything he does. He's one of the most accomplished warriors in the FFVII mythos and not to be fucked with, regardless of his SOLDIER treatment; after all, natural talent and ethic does factor in the end, given that SOLDIERS have different ranks according to strength and skill.
Cloud however, is just that dude, despite being, by most definitions, a loser (although one of my favorite characters, so that isn't negative bias. But I mean yes, he is a dorky loser), is a freakishly talented and superhumanly strong individual that constantly defies expectations quite casually, even before his SOLDIER treatment.
I think Cloud is stronger than Zack, but that doesn't mean Zack is weak, either. Cloud is just on another level.