I have no doubt that if Canon had developed a 12mp FF sensor for the mkIV that it would match the D3s.
If there were a way to turn off the in-cam NR in the D3s, you may find it matches now.
I'm only at odds with the fanboys expecting it to be as good or better than the D3s at high ISO.
Of course, if you have one sensor that has 64% more light hitting it per unit time, you expect that sensor to perform better at high ISO. The confidence exhibited by some so-called Canon "fanboys" is based on Canon's apparent superior sensor technology, which allows efficiencies to somewhat close the gap. By how much, we don't really know yet, as the D3s advantage may be more due to in-cam NR than FF large pixels. And that in-cam NR, while great at removing chroma noise, may be actually producing a less detailed image than if the user were to judiciously apply NR themselves.
I'm sure Canon could have produced a 16mp FF that still pushes 10 fps that, with the efficiency advantages of the 1D Mark IV, would give it superior ISO performance to the D3s (in-cam NR or not). There are those loud few who would have preferred that. But, at the same field of view with the same lenses, that would crop the shot back down to the same 10mp as the 1D Mark III, so it wouldn't be an improvement in the detail of many cropped shots.
I suspect Nikon retained the relatively low 12mp in the D3s, because they don't have the processing power to push more than that at 9 fps (not without an expensive processor upgrade at this time). Canon's 1D Mark IV is pushing 160 mp/s vs. 108 mp/s for the D3s.
I'm sure Nikon's D4 will have improved processing power that will allow more pixels to be pushed, and it will have more pixels to the dismay (or total indifference?) of the low-rez Nikon fanboys. As Nikon adopts what Canon has been criticized for, the criticism falls away (i.e., CMOS, FF, High ISO performance, 14-bit, etc.).
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Tacksharp