I think that Zeiss 28 F2 lens is limiting the D800E somewhat, particularly for the infinity landscape comparison. As I recall, that particular lens is not really that great at longer distances. I have also seen much better detail from the D800E with other lenses and in other tests, for instance here (look at example 4 for wide angle tests):
Anyway, the Leica lens on the S2 is obviously better and the D800E is extremely demanding when it comes to lenses (yes, even this Zeiss lens is not perfect!).
On the "bokeh test" picture of the M camera, he says there's no LoCA from the S2 - but I see lots of green?
The watch photos are focused differently. The D800 pic is focused on the watch hands, which are sharp - you can see the individual pixels there. But then most of the watch face is slightly behind focus, and hence has green LoCA.
The S2 pic is focused ever-so-slightly behind the watch face. So the hands are blurry but the face is generally in better focus than the D800 pic, though it's got a slight red fringe.
