For me, the IQ on the D800E is such a knockout and DR so great that as far as I am concerned, sensor wise, unless you want really huge prints (over 40") or extreme colour fidelity (as Jack points out) then the D800 is a no-brainer at the price when compared to the backs. It is easier to use and more flexible too.
BUT as Dave has said, getting edge to edge sharpness is harder. The lenses on offer are much wider in variety and character, a bit lighter. on average a little cheaper (though that will change) but none of them can do what a great Schneider or Rodie can do. As Jack points out, that may not matter but if, to you, it really does, then MF still has an advantage.
My IQ180 is still on sale at my dealer and there isn't a week that doesn't pass when I consider retrieving it. The rub is, that it is only on a tech cam that the results are so clearly superior that there's a real difference in prints under 40" and my favoured tech lens, the Schneider 35XL, doesn't play well with the IQ180 so I would have to shell out $,000s for a Rodie that does. Which money I would rather conserve for D800 glass. I would add that my recent addition of the Zeiss 21mm F2.8 and the Samyang 14mm f2.8 have really swung me back in favour of the D800. On both, there are apertures and focus distances that can get everything in focus and at lovely resolution and micro contrast.
Having said all that I still sometimes, rarely, have the urge to print to 1.5 metres and in that regard, the IQ180 is the only game in town if you want the highest quality...