Early early stages for me but D4 AF appears to be superior on long lenses with teleconverters. By this I mean initial AF acquisition.
D4+500VR+TC17E just hold the rig up and AF snaps into focus on my BIF. Boom boom boom, the thing just never quits
D800 does not acquire initial AF nearly as quick from very limited experience. It also gives up far more often (fails to achieve), so I have to point it at something else at a similar distance and with better contrast to get it in the zone, then repoint on subject, acquire AF, then shoot.
I'm not talking down light ideal situation (all our DSLRs are good at that). But the tough, light angle is wrong, using a long f/4 lens with a long TC (TC17), bird and lighting are lower contrast than ideal, D4 is snappy snappy snappy. D800 I have to work it, refocus on something else. Not sure what D4 is doing but it is a lightning machine and of course the fps and buffer just add to that whole experience.
I am currently considering D4 as perhaps my better BIF tool and D800E as non-in-flight bird tool.
Don't take as gospel though, I've had my D800E for a week, and D4 for 6 months. Not sure about AF tracking after initial AF acquisition, need more experience but I do intend to critically evaluate that too.
The other thing that occurs to me to be careful of in drawing this conclusion is this noted difference may not apply on lenses shot native (as opposed to with TC at starting focal length of f6.7).