Ha, sounds like you’ve been reading too much Ken Rockwell (he basically argues that we’re all being duped into spending more money on high-end Nikon DSLRs, even given that they all use the same internal parts and processors).
Having experience with both, I can confidently tell you that the D4 is much better IMHO. Although my D800 (which I’ve since returned) didn’t have the dreaded left-focus point calibration issue, I found most of the focus points outside of center to be unacceptably soft (tested using a 35mm F/1.4 and 24-70mm F/2.8), whereas my D4 is tack-sharp and spot on. Of course, this could be a calibration issue – and I’m making these statements based on only one test sample (although online user reports seem to mirror my sentiments).
I think the D4 focus is just faster, tracks better, and does a much better job of locking in on low light subjects (The D4 does have amazing low-light sensitivity down to -2EV). And with the recent D4 firmware upgrade, AF-C tracking is further improved.
I suppose it depends on how you’re going to use the focus? If you’re a tripod guy who works in Live View using pro glass, you’re probably not going to see much of a difference. But if you’re handholding or tracking a moving subject (in lower light), I believe the D4 blows the D800 out of the water.
Don’t ask me what magic Nikon uses to tweak their Multi-Cam 3500-FX AF engine, it’s just better on the D4. Technological advantages of the D4 aside, if you add in all the caveats of shooting at the mind-numbing size of 36MP, you’ll generally find a much higher focus keeper rate using a D4. For example, I can shoot at 200mm using 1/250s on a D4 and be completely sharp, whereas the same focal length on a D800 might require 1/500s or higher to achieve similar sharpness. Regardless, I’ll take the D4 focus over the D800 focus any day of the week.