Marianne and I travel with 2 camera bodies and a backup when we go on trips, however, our previous set up was that of 5dmk2 , 5dmk3 and 7D backup.
Given that I wanted to use one body for work and the backup works best as a full frame unless we bring along another backup wide angle lens, we opted to get a 6D body.
I used the 5dmk3 and 6D for about half of the most recent trip each and here's some of the initial experiences
1. Body : 6D smaller, lighter and if set up as 6D +17-40 vs 5dmk3 +16-35mm, the 6D setup is much more compact. This means that that's my preference for taking it on treks where I'm looking to minimise weight (eg multiday hikes)
2. Ergonomics: all of the buttons are on the right hand side of the 6D which takes a bit of getting used to and I'm not sure if it's better. The joystick on the 5dmk3 is far superior to the rather flimsy feeling 4 way joystick sitting on top of the dial of the 6D.
3. AF : 5dmk3 clear win with options for AF points - I haven't been able to test the reportedly better 6D AF in very dark settings
4. Image quality: Suprisingly at low iso, I notice a little bit of noise on the 6D (very slight) but at high iso, the 6D does VERY well , in fact, I'd have to say at least on par with the 5dmk3 for the star shots that I took on the trip.
5. Post process: I find that the 6D files cannot be pushed as far as the 5dmk3 files in terms of colour adjustment or highlights and shadow adjustment. This may be a good thing in terms of keeping me from going too far with post processing but from what I've played around with, artefacts do start to appear earlier.
6. Weather sealing : thankfully I've been paranoid enough to not test this by keeping the cameras protected.
My verdict - if you are a landscape photography solely and into night photography - I can't see much reason to fork out the significant extra $$$ for the mk3. If on the other hand, you do other genres of photography (even for me, taking pictures of Charlotte are much easier on the mk3 due to the AF options) which might be AF dependent, then the 5dmk3 is clearly ahead.