I have both.
If I didn't own a 5D3, I would feel the 6D was fantastic, in fact I often prefer it over the 5D3 for shots where I have more time.
But the 5D3 is over all, far supirior as you would expect for twice the price. Not in image quality, but in ability and features, other than wifi.
However, other than faster action and possibly some low light situations, there isn't any thing my 5D3 would have got that my 6D couldn't capture equally.
I use both together with different lenses, I have often thought of selling one to get identical bodies, purely for the convenience of identical layout and control, and if the 5D3 had wifi I would, but they both have unique benefits so the trade off is different capabilities/uniform layout. At this stage I think I'll wait for the 5D4 and trade up both if it has wifi.
If I shot only landscape, still life or even portraiture, the 6D would be my choice.
If I shot only sport, wildlife, active kids or more environmental type portraiture, the 5D3 would be my choice.
But I shoot enough mix so they compliment each other. Different tools for different jobs that over lap to cover most situations.
Comparing the 6D with the 5D3 is like comparing the 5D3 with the 1Dx, in some respects the 5D3 is better than the 1Dx, but in other aspects is not.