There is in-camera HDR. We don't know what that is, but it sounds promising.
There is a 1.2 crop mode for a little extra reach but qapprox 24 mp images.
Like the D4, the 9 cross sensors will AF at f/8. That should mean improved AF with existing f/4 lenses and the 2.0 teleconverter - or stopped down.
The D800 is keeping the 10-pin connector - a nice plus and helps avoid the need for still another cable. The connector is still on the front of the camera which is better with L-brackets than the side positioning of the D7000 USB.
The D800E is addressing AA with software - and possibly hardware as well. (if just software, why the price increase and why not make it a standard menu option?) We need more details. The moire removal tool in CNX2 might be useful for other situations.