As a general comment to the whole discussion I would say that:
The best cameras today are probably good enough if you put a decent lens on the body, use tripod, minimum ISO, mirror lockup, cable release or self timer and focus using live view or a 30X loupe on ground glass shimmed into alignment with the sensor. If you don't do that, why care?
If you do all of the above you may find the best lenses. You can buy a Nikon D800E and a bunch of Zeiss lenses for 6-7000$ and feel assured you have about the best of stuff in the DSLR market.
You can choose to spend 3-5 times the amount on MFD equipment and achieve some real or perceived benefits. Obviously there are couple of benefits of a larger sensor. It will probably collect more photons, unless the vendor of the smaller sensor makes some magic with full well capacity (FWC). A larger format makes also less demand on the lens.
Now, Nikon and Sony developers do some magic with FWC. Check http://www.sensorgen.info/
Nikon D4: FWC=117813
Nikon D800: FWC=44972
Hasselblad H3DII50: FWC=38463
PhaseOne P65Plus: FWC=53019
So although the Nikon D800 has small pixels, FWC is similar to some relatively recent digital back. This may mean, if sensorgen information is correct, that the latest generation of Nikons are very good at collecting photons.
But any way,it is your money, and as long you are happy with the results you have, it is just fine.