Actually, it's BOTH the slight imprecision of the AF system (when discussing wide open apertures) AND the demanding nature of that much pixel density...
Note carefully that I've had no problems with the AF at the regular and usual apertures - studio work, outdoor work, no problems. But when I've run tests with my fast lenses (24/1.4, 35/1.4, 200/2), at wide open on on each of them, in moderate light, focus precision / consistency has not been as good as with the D700. Again - note I said "wide open". Put the 35/1.4 down to F/2 or F/2.8, and there are no problems. Put the 200/2 down to F/2.8, not a lot of problems, and so forth. For some reason I think the tolerance of what the AF system in that body determines as perfect focus is a bit "loose" and thus when you shoot with a lens that has terribly thin DOF, you'll have some OOF frames.
I don't think this is what is causing most of the issues I read about:
I think what most posters are experiencing when they have OOF issues are a few things:
a) the focus area "seen" by the AF sensors is slightly wider than what the little square in the viewfinder shows
b) people focusing on things where there is, from the cameras point of view, a "better contrast scenario" within the area seen by said AF sensor (which is wider than the square in the viewfinder) and thus the camera latches onto that "better" scenario since it doesn't really know what the user wants.
c) because the sensor has a lot of pixel density and people blow everything up on screen to 100%, it's more obvious when something is out of focus - thus, if you aren't focusing correctly, or are moving when you take the shot, don't have sufficient shutter speed, etc, you'll notice it more.
Great camera, but one that demands more precision than a lot of people are giving it.
So it's two different things - wide open focus in-precision (is that a word?), but that's different and I don't think what causes most people pain. The A/B/C I gave above is what is causing most people pain, I think.
-m