I have a 60D and have got very fluid with it, altho the 9 AF points all correspond to a spot on the D-pad. 11 Is going to be interesting to choose with a D-pad.
Overall I like the control layout of the 6D a lot better than the 60D, although it takes a bit of getting used to - I've had it for a week, and I'm still pressing the wrong buttons out of habit. However when it comes to AF point selection it's just not as good. The 60D was really fast with the D-pad + set button. The 6D doesn't work like that. You have to "scroll" through the points, and the diagonal buttons are almost pointless, since you normally hit one of the other directions instead.
Since this is a positive list though, the way the zoom button works is awesome. You can set it to default to any zoom level you want, and with one press check your focus. Way faster then the 60D move your thumb all over the place dance.
Other button notes: the buttons have a nicer "feel" to them. They feel a little more real, like you are actually pressing something. Although on the D-pad this seems to have made the diagonals impossible to hit as noted above. The DOF preview button while still in a bad location, feels much nicer.
And switching to movie mode no longer takes a stupid amount of turning.