Not much to say that hasn't been said but I want to compliment you on the shots. I think anyone here would be glad with these results. You did a great job. Tweak all you want but you are improving on a very good product already.
Right, that's what I wanted to hear, 4000+ posts on CR have finally paid off :-> ... thanks! Btw this is about the same feedback I'm getting from around here, that's why I currently dare to try to go pro with pet and animal photography.As for the 6D AF system and whether a 5D3 would make a difference... rest easy. That ain't it. I think you know better than that. The issues you are dealing with here can't even be much affected with manual focus. It's definitely NOT the camera
That's very good to know as you know both cameras, it dampens my 5d3 inferiority complex a bit :-p ... the other day, I saw the boss of the homelesss peope street magazine project walk about with the editorial 1dx+24-70L2, I couldn't believe my eyes. He still takes terrible pictures and doesn't even use a single flash :->
The one thing might help just a bit that with the 1dx/5d3 af focus & recompose distance is a bit less than from the center 6d spot, but alas, the af points are rather crowded to the center on the big cameras so it really might not result in any noticeable difference.
Think about the cameras this way... if someone handed you a 30D or a 40D, would you still love shooting with one? Could you still make great pictures with it? Heck, would you almost be ready to go find/get another one? I'm confident that my answer to these questions is YES, I loved both of those bodies and shot 1000's of great images with them. Obviously my newer cameras are EASIER to shoot with because they have better sensors and the full frame gives me more creative latitude.
Bottom line, it's YOU that takes the picture. And it sounds like you could shoot the same great shots with a 30D, 40D, 6D or whatever you have in your hand. (Too bad the guy with the 1Dx can't say that, eh?) My point here is, don't pine after the 5D3 or 1Dx too much. I love the 6D, it's a great camera. Don't sweat it. Be glad you have the 6D, enjoy using it with confidence and without any remorse!