I would say at specifically ISO 1600 and ISO 3200 the D3 is about 70 percent of a stop better. Not quite a stop, but enough for face details to stay intact in printed large albums. Something that does not happen with the 1D3 - but DOES with the 1Ds3 simply because of it's file size even though ISO 3200 is not a profiled ISO setting that complies with the normal range of the camera.
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That's not clear. Are you saying that the D3 is one stop (or close to one stop) better than both the 1D3 and 1Ds3? Have your comparisons involved same exposures at ISO 1600 and 3200 (with all cameras), same image sizes and appropriate processing of RAW images rather than in-camera processing of jpegs?
The main reasons for using a high ISO are because the subject is not completely stationary or (if the subject is stationary) because one doesn't have a tripod for the long exposure that the poor lighting conditions require.
In such circumstances, the choices are, when flash is not available or appropriate; risk getting a blurred shot using a shutter speed that is too slow; risk getting unacceptable noise and a tonally degraded result by using a high ISO setting; don't take the shot.
My concern would be that some photographers using a D3 might happily take a shot at ISO 6400 and get acceptable results for their purposes, whereas other photographers in the same situtaion and with the same purpose in mind, but using a 1Ds3, might be deluded into thinking that the shot is not worth taking because their camera's maximum 'real' ISO setting is only ISO 1600.
It's a big assumption to make that a 12mp camera at ISO 6400 is likely to produce a better picture than a 21mp camera at ISO 1600 underexposed 2 stops (or at ISO 3200 underexposed 1 stop).