The highly respected Bjørn Rørslett has posted an answer to a blog entry by Lloyd Chambers:

“I’m having trouble making acceptable photos with the D3, everything  seems soft and just not ‘there’ ”
(Source)

The answer:

“The first D3 advantage obviously is a vastly improved noise performance, the second that the combination lens + camera can achieve higher image contrast thus imparting a better sharpness for the “big details” that give the overall impression of sharpness of the image, the third (deriving from the second) is that the files stand much better enlargement. The almost total lack of CA and the even illumination of [some, not all] wide-angle lenses might result from the sensor design or the EXPEED processor, or both.

Now, to the drawbacks. It is clear that with high-performance lenses, D3 might have insuffcient resolution due to its lower pixel density. Whether or not this is an issue will depend on the subject and scene contrast, and also the processing of the file done in-camera. Shooting people with D3 should yield remarkable image quality, landscape shouldn’t.”
Read his full answer at the NikonGear forum.