I am beginning to think I am the only one who got a flawless 6D. At least have not come across any issues yet. I have my fingers crossed.
Mine's been great too. Depending on what body the OP was coming from I can see his frustration. If he was coming from a 7D, then it makes sense he's complaining about the AF. If he was coming from a T2i or similar, the 6D, mine at least, smokes it for AF speed.
However, I put my 6D though a scenario I knew it would lose yesterday, tracking my dog running flat out towards me after a ball my friend had thrown. My old 7D jumped at this opportunity nailing every shot, the 6D returned 1 of 6 shots tack sharp, 2 sort of acceptable, and 3 not at all acceptable. This was using centre-point only. Although I was able to shoot at 6,400 cleanly to stop motion, which I couldn't have done with the 7D.
The fact of the matter is, I knew going in that I'd lose AF ability with the 6D at the gain of better DOF control and low-light capability. I also gained $500-800 by not going 5D3. I don't often shoot high-speed action so it was a good tradeoff for me. It is good to know the limitations though.
My first 7D had an awful image quality. The second, is quite ok.
I was disappointed by the slow Autofocus of my brandnew 6D. But this is not normal, it is an technical problem that occured. 2 seconds to get sharp. Second, the AF fields had an red corona and sometimes did not disappear - and stayed lighted.
Your thoughts were mine, too. It bought it as an second body to get better image quality for stills, macro, available light, landscape.... specially if there is not much light.
p.s. And the "he" is female.... I have met her.