With the 6D you settle for a less robust AF system, no second memory card, etc. to save roughly $1,000. For me and many others that's a good trade off.
Fyi: I'll buy a 6d, too, so it's not like I'm opposed to it. It's just that I don't expect to be able to take very different shot swith the 6d vs. my current 60d, actually I'm loosing af flexibility and reach but am gaining high iso iq.
With the 5d3 af, I'd be able take completely other shots where my 60d af simply fails - so the 5d3 doesn't have a more "robust" af system, but a really different level. I think it's currently wiser to invest the 6d/5d3 difference into filters, lighting gear and other accessories that won't loose value.