If we forget other reasons like large bright viewfinder (which I find quite important), synch time, ... and concentrate just on IQ, here are the reasons why I own and use the Leica S in regards of IQ:
-better skin tone and color
-smoother transition from focused/sharp area to background
-smoother color transition
-more 3d look (might have to do with the transition)
-very good DR
-How much is from sensor quality? How much from sensor size? how much from lenses? How much from profiles? I dont know, but I just love the IQ.