Here is one of those im not really helping but thinking out loud posts
Coming from a 60D...
I dont think you can go wrong with either one of them honestly. Lets just assume $1000 difference for the sake of argument.
Warranty clarification aside, I got mine for $2499 (US Model) and no tax so it would have only been a $200 difference for me as a NY'er (Amazon, BH etc). So it was probably the biggest reason I went with the 5D3.
The 6D had everything I long desired for FF, low ISO performance, AFMA etc. I didnt know if the AF would be a big deal for me until I started playing around with it.
I was experimenting tracking one of the blades of one of our ceiling fans last night at a low rpm setting using wide open aperture on my 50mm and was impressed of its ability to lock and be in focus. Probably not an ideal test but lighting was average so its an definitive improvement for me from the 60D. Plus I have an 18 month year old who wont sit down for anything...
Didnt check to see if the 6D had HDR and multi exposure built in, but actually dont find the multi-expose as gimmicky as I would have though.t
Like I said $1K more dont know thats hard when you can grab a 100L or 135L with change