The problem is Zoom doesn't need to physically defeat Prime. Stealing his speed to the point where it will take him a century to blink..I would consider that a victory, and Zoom has recently shown he can lend and steal speed just like Wally, although I'm not sure if the way they accomplish it is the same.
Prime reacted to a blitz from a couple flashes, but he wasn't outright owning them in speed. Zoom was causing sonic booms simply by snapping his fingers, and was vastly quicker than someone who can evacuate a city of 500,000 people in less than a second. Wally needed to steal the speed of 2-3 other speedsters to simply get on Zoom's level.