I dont think it really matters. A D3 in the hands of an absolute beginner doesn't make a difference, while a D3100 in the hands of an experienced professional could still produce stunning images.
At the end of the day, you're just looking at features and capabilities. The D90 offers independent dials for shutter speed and aperture control, plus the benefit of an on-body motor (so the AF-D lenses work just fine), and separate buttons for exposure compensation. All this, and still has 'easy' modes for Action, Portrait, Landscape, No Flash, etc. And it has Commander mode to wirelessly control off-camera Nikon Speedlights. High ISO performance shows its limits at ISO1600, and personally, I find ISO3200 to be pretty much unusable. Still, with creative use of lighting, you can still do quite a bit and not blow stupid amounts of money. 12.3MP is still a lot of pixels
Bottom line is, a good photog would put the D90 to good use, while a beginner would not easily recognize the benefits of a D3x.