It is virtually impossible to replicate photographs taken with different cameras but with the same ISO, aperture, and speed settings, and therefore making judgments based on the comparisons are ill-informed.
I have read this thread and discounted the red herrings, and here is some commonsense.
ISO, aperture, and speed settings are consistent across manufacturers. This is because there are international standards of measurement. For example, some photographers may know that the term "ASA", in referring to film rating, stood for American Standards Association. This is why an ISO range for a DSLR conforms to the standard, but the "extensions" do not. Speed, of course, is a measurable standard. So is aperture, and here is where I take exception to one comment made: "F-stops are just geometric ratios and don't reflect actual differences in light transmission." I had to read that several times because I just couldn't believe someone would say that. F-stops ARE the measurement of changes in aperture and thus DO reflect actual differences in light transmission.
Having said all that, if I take a remote shot with my 5D2 at 1/200 second, f8 at ISO 200, then take the exact same shot half an later with the same camera and the same settings, the second image WILL be different from the first. Why? Because the light has changed. Moreover, due to the 5D2's rather limited AF system, unless I dictate the focus point, the change in light may cause the AF system to focus on a different part of the image second time around.
In your example, I note you used the remote trigger. In other words you had no way of knowing what the AF was doing. I note also that you were in a studio, so I will assume the light conditions when the D3 did its thang were EXACTLY the same as when the 5D2 strutted its stuff. But even if that assumption is correct, you simply cannot compare the AF system of the D3 with the 5D2's. One is infinitely more refined than the other.
But what about the light AFTER it passed through each respective lens? Does the D3 have the same sensor as the 5D2? No. Are the pixels the same size? No. Is the noise performance the same? No. (Starting to get my drift?) Were you using the same lens, ie with the same aperture mechanism, same number of blades, all rounded? No. Were you both shooting in RAW? Because if not, the discussion ends right there.
But even if you were both shooting in RAW, what adjustments were being made in-camera by the D3? Who knows?
In summary, yes, ISO, aperture and speed are constants. But everything else isn't, rendering comparisons pointless and any conclusion that one camera is better than the other - unsound.