Shake Shack is clearly superior. I just tried it for the first time. Been to In N Out many times when I lived in San Francisco.
Shake Shack's burger was bigger and not well done. It had more of a grill-y flavor. The cheese was perfect consistency. The bun was a delicious egg bun.
Shake Shack's fries were crinkle cut and crispy but soft on the inside. They tasted like potato chips in fry form and had some kind of other seasoning.
Shake Shack's chocolate shake was yummy. I'd say SS shakes are about the same as In N Out, but I have only had an In N Out shake once, many years ago.
Also, Shake Shack sells booze. Score!