I would take 5D II out of the equation for one reason, fixed auto ISO @ 400 in "M" mode.
6D or 5D III
A. Take 5D III if you want to have the best AF system
B. Take 6D if you plan to shoot center AF with slightly less precise
+1 for not even considering the mk2. The fixed ISO...well, manual ISO in manual was annoying when I borrowed a friend's mk2. I'd prefer to at least have the option to set shutter and aperture while letting the camera decide on ISO.
I vote for the 5d mkIII. no regrets here. no looking back thinking I could've/should've gotten something better. Save a little longer!
As far as the more complicated AF system is concerned, it's got more options, yes, but that means more flexibility. It took a little reading, a little shooting, and a little tweaking to get used to the whole new AF system but it was worth it for me. You can dumb down the 61 points of AF by using AF "Zones" instead of AF "Spots" or AF "Areas" so that the AF selection acts more like the 9-pt AF system in my 60D. It really isn't that much info to read up on.