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Strange, even my EOS 450D gives me reliable, accurate PD AF. The newer Canon models are even better (5D mk III, 60D, 650/700D, 1D X, 6D). I even get accurate focus with MF lenses relying on focus confirmation with PD AF (Nikkor-H 80mm f1.8, Nikkor Auto 55mm f3.5 micro, Ultra Micro Nikkor 55mm f2). Even my Sigma 18-50mm f2.8 EX DC, which was a total disaster on the 350D concerning AF accuracy behaves pretty well on my 450D.

 

The D800 seems to be a step back from the D700 and D3(S), a while back I have read (in some dpreview forum thread) that it does things with points around the AF point you are thinking you use, which causes surprising AF results at times. And this causes frustration with users. 

 

Try a different DSLR to notice the difference.

 

The D800 is my first Nikon camera so I can't tell whether it's better or worse than a D3/D700. The thing is because of the high pixel density and the fact we can check results at 100%, focusing errors, even very small will be more noticeable on a D800 than on a 12MP camera. Additionally, unless  you print quite big, it's unlikely that on a D800 any small AF error will be visible.

I used to have a K5 and the issue was actually much worse (AF was the main reason why I left Pentax actually).

 

The mere fact of the existence of micro-adjustments clearly shows the issue is very real. This is the (dirty) fix manufacturers have found in order to allow users to correct for AF calibration issues.

 

Of course, focus issue is lens dependent and once a lens is calibrated (I use FoCal which is pretty good to semi-automate the process), it gives great accuracy. However, despite this, focus is not always reliable and consistent which forces me to usually take several identical shots "just in case". Moreover, FoCal recommends users to recalibrate their lenses once a year, because of AF drift over time.  When it comes to AF calibration, fast zoom lenses are a real pain: take a 70-200 f/2.8 lens for instance. Chances are that you'll need say -5 AF adjustment at 70mm and +4 at 200mm.  What do you do then? You have to bias the AF towards the focal length you use the most or choose something in between where the center of the range will be spot on while the short and long ends won't be perfect.  That's just great!

 

Working on the final image is really the strongest point of mirrorless. It doesn't matter if the focus sensor is not perfectly aligned since you work on the final image.  You don't need to review your shots as you know they'll be in perfect focus.  Camera/lens calibration is a thing of the past.  It's just so much better and enjoyable to use.

 

Maybe I'm particularly picky, I don't know. I'm just starting to be really fed up with this whole PDAF crap.