My experience comparing my D4 and D3 with various lenses shows the D4 to be superior. A good test is photographing a person's eyelashes (eyes closed). After adjusting AF Fine Focus on all my lenses, I found the D3 to not be as sharp as my D4. I also found that my zoom lenses are not be as sharp as fixed focal lengths. In fact my Sigma 85mm f1.4 is superior (with respect to sharpness) to my Nikon 24 - 70 f2.8 at 70mm and f4 on my D4.
I believe the additional pixels of the D4 account for the enhanced sharpness of the D4 over the D3.