This "3D" experience is a bit underdefinied, IMHO. What does it mean, any samples with and without the "3D" effect?
Now, a larger sensor comes with some advantage. Any detail will be larger on the sensor surface, and magnification will be higher. The amount of contrast transferred by the lens is higher for larger details than for smaller ones. So for small details an MF lens will transfer more contrast.
Finally, the lack of AA-filtering will also keep more fine detail contrast
. It will also induce fake detail
, which may add to the perceived quality. A typical example may be that feathers on birds may have finer structures than the sensor may resolve. So the feather may essentially just be a gray mass. Now if the lens can transfer say 35% contrast at the pixel size some of that contrast will be reproduced as low frequency aliases, that is fake detail. So we see patterns in what would be gray mass.
Regarding the 5DII I would say it was a fine camera and still is. I don't know if the Sony Alpha 900 is a better camera as I own an Alpha 900 but not a 5DII. The Nikon D3X has better DR, and that may matter in some cases. I may add that it may be that the Nikon is simply better.
A very good comparison of MFD and Nikon 3Dx is here: http://www.luminous-landscape.com/forum/index.php?topic=50977.0
I have noticed a quirk in this thread and some others: discussions of DMF vs 35mm digital that involve lots of "DMF is better than the Canon 5D" comments. There was a time when the 5D Mk II gave arguably the best image quality in 35mm, and at a great price, so maybe that lead many MF users to choose it as their 35mm alternative, but that time is past (since the arrival of the Nikon D3x and Sony A900). I for one am going to wait until some good photographers with DMF experience have put the Nikon D800 and D800E through their paces.
One question I look forward to: is it the aliasing effects and/or less smoothing at high contrast edges due to lacking an OLPF filter that leads to the enhanced "htree dimensional feel" often artributed to MF? Some kind of enhanced accurance? I wonder just because one person has said the same of the D800E too.