In terms of quality, my view is that, judging from the current samples, the output of the D800E is in the very same ball park as the S2, 645D and P45+, Leaf, H4D40... I am 99% sure that they would be impossible to distinguish at any print size.
While not all can be seen by JPGs... the D800E is of a different design than S2, 645D and all you mention. Thus there will be differences no matter what, and with benefit to the larger formats, but of course depends on light and subject and more. The JPGs are not bad, but there is no way I can see image quality (low ISO) being better than even the 28MP Leaf which I prior owned. Yet, they are different tools. Looking at the samples I frank believe the image quality from 22MP Leaf Aptus 22 is very easily capable of higher image quality at low ISO, but of course with lesser pixels. DR/NR, for DSLR that is also performed inside the camera in a black box. How well? Actual comparisons will tell later...
I would guess that the D800 sensor will outperform current MF sensors even at low ISO speeds, with greater dynamic range at minimum ISO due to the far lower read noise of current CMOS designs. If so, apart from the inertia of photographers who own gear of a certian brand and format and out of familiarity can work better with it, the longer term future of formats larger than 36x24mm probably relies on two things:
1. Even higher resolutions (serving the needs of an ever smaller proportion of photography)
2. Better lenses, both to keep up with ever higher resolution and with better control of distortion, corner performance, bokeh, etc.
Oh dear... D800 outperform current MF sensors even at low ISO speeds... Nope, nope, nope. Doubtful at best, if not impossible. Sample are very far from it (+1 on plastic, lack detail).
It is not only about pixels folks, although the more pixels are part of the equation.
1. Yes more pixels, but also further improvements in image quality. That go for all medium format, DSLRs and cellular phones!
2. Lenses of all current medium format systems more or less already have the better lenses. The more critical will be for DSLR lenses, since the format is smaller.
Above said, it is really good news for DSLR users with the D800 / E, congrats