One would certainly expect this to be the case, but often things are not what they seem to be. For example, the D3's ISO 12,800 and 25,600 settings are apparently bogus. The purpose of having them is (presumably) to make assessing correct exposure in the histogram and the camera's LCD much easier. The jpeg image has been adjusted, in-camera, despite real and actual underexposure. Without such settings, one would be squinting at apparently underexposed shots in the camera's LCD and trying to judge if the shot was really too much underexposed or not.
I think also the purpose of these ultra high ISO settings relates to ISO bracketing. I'm not sure about the features on Nikon cameras, but I believe they've had ISO bracketing for a while. Of course you can't bracket an ISO which doesn't exist.
For example, if I take a shot with my 5D at ISO 3200 and the histogram and highlight flashing tell me I've overexposed, I've ruined the shot. If I need a particular combination of aperture (for DoF) and shutter speed (to freeze the action or camera shake), then autobracketing of exposure is not a good option.
Without ISO bracketing there can be a disadvantage in using an 'ersatz' ISO setting.
Since Nikon is now offering these 2 ultra-high settings which are really underexposures, it's quite likely they have built in a level of noise reduction to make them more acceptable. Once detail has been lost through in-camera noise reduction, it cannot be regained.
However, there is now a way of reducing noise, not only without destroying some degree of resolution, but with actual enhancement of resolution.
I'm suggesting here that using such stacking processes with ultra-high ISO shots, the D3 might not even equal the 5D. It's something which I think should be tested.
I haven't used the D3 yet, so i don't know, but do you have evidence of this, or is it an assumption?
My 5D does have low noise levels, but 3200 makes a jump. More so than from 800 to 1600, so what you say could be true in regards to the 5D.
But, it seems to be quite a step to go one from stop further in underexpose, to two stops.
From what Michael has shown, and from what I've seen on some other sites, even 25,600 looks to be noisy, but usable. I haven't tried underexposing to get to 6,400, but somehow, I don't think the noise, and lack of shadow detail, would be as good as the Nikon at 12,800. But, now, after all of this talk, I will see if I have time tonight to try it.
The supersharp techniques seem to be interesting, but are not really useful under most conditions. It's too specialized, more so than the HDR tecniques I use.
No matter what we want to do, the capability of the camera itself is still the practical limiting factor. The 5D has the greatest dynamic range I've seen outside of the Leaf backs I test for Leaf. I assume other medium format backs also have great dynamic range. But, these backs rarely go above 400, and I've not tried to push them further.
It's an interesting topic, and so maybe I will try next week, with the Aptus. The problem pushing any camera beyond what the manufacturer specs, is that the RAW converters are set up to process these files only according to the limits set up by the manufacturers, and moving out of that parameter range might result in unexpected deterioration of the image.
No matter how we look at the 5D vs the D3 (and this is from a Canon user since 1969 when I went to Phokina and saw the new Canon "F".), the Nikon seems to have at least two "real" stops of ISO extension, and this is very significant. Canon will have to catch up. Hopefully, a 5D replacement will show up in late Feb, or March, and will make up one of those stops, with a "normal" range going to 3,200, and an extension to 6,400. This would satisfy the old Tri-X at 1200 with Accufine person in me quite well.