I have a pair of D4's and a D800E and I kind of agree with you. I have had no focussing issues with the D800E but when I really want to be certain of results, I am reaching for the D4's.
I find that the main reason is just the way the body sits in my (large) hands. Added to that is the fact that I do mainly nature photography including a lot of macro work in the field. I just do not feel confident about the weather sealing on the D800E - even though I have no real reason to doubt it.
The real argument that I have had is about glass. With the D800E I can crop or use in-camera crop to get to DX and the additional apparent reach. Do I carry the 400 f 2.8 or the 300 f 2.8?.
I am increasingly carrying the bigger lenses (thank you Mr ThinkTank for my Lense Limo).
But when I nail it with the D800E I am also very happy ..... I think what I really want is a D4X so I can crop insects until I am happy and not lose resolution.