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Ahh.... I see where you're coming from and for the most part, I agree. I had some stunning large prints from my 6mp d70. I assume that you want to crop the d3, because you're looking to the DX crop factor for reach. IIRC, that gives you about 5MP.
At the lower ISOs of the d3/d700, you'll have very clean images, so there won't likely be any difference between the full and DX crop, which is what I was getting at the first time. But, IME, AF is not as reliable as the noise performance of the sensor. I much prefer to use the full image, rather than cropping, simply due to focus inaccuracies that often come into play, especially at the higher frame rates on moving subjects. Those inaccuracies are magnified with DX crop, which is also what I was talking about earlier.
Given a choice, I'd much rather shoot a DX camera than try to use an FX camera in DX mode. That's why I still have my d300 to use with my d700 and d3s. In low light, high ISO situations, I'll use the d700 and d3s, with a 1.4x TC on the d3s. I also use the 120-300 Sigma, but it can also have misfocus issues. There are sometimes issues with the TC, but again, IME, I have more keepers, better shots with the TC rather than just cropping the image or using DX mode.
Perhaps that may not hold true for users with the 300 f/2.8 or the 400 f/2.8. Maybe those lenses get a much better focus lock than I can get with the 70-200vr or my other long lenses. I assume that they probably do and maybe that would give a higher DX crop keeper rate, but I don't know for sure.
I hope that is the information you're looking for.