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.