dustin created an excellent thread on the 6D ... Here -
Yes, i found Dustin's extensive breakdown review and large corresponding thread recently, and after reading it it really made me wonder about a 6D again (after going back and forth a few times). He has a compelling argument, but again, he's apparently not that familiar with the AF system on the 7D, and therefore what the 5D3 makes use of.
What I am mainly worried about is if I go for the 6D, i'll find the alleged shortcomings too distracting, and ill be pining for the 5D3 anyway. The cost is the great equalizer though.
I have both the 5D3 as well as the 6D (also had the 7D till last year). The biggest shortcoming of the 6D (as compared to the 5D3) is the autofocus and coming from the 7D, it might feel like a slight let-down.
IMHO, all the other differences are just gravy with quick workarounds available for most shortcomings on the 6D.
What I would advise is you need to look at yourself as to what sort of buyer you are. If you are one of those who want the best, buy the 5D3 or else the longing for the 5D3 will almost always remain. However, if you are one of those to whom gear doesn't matter (beyond a point), get the 6D.
PS: I personally find the files of the 6D a tad cleaner than the 5D3.