Canon beats all except for more mega-pickles and low ISO DR (although not much natively)... i.e. Not pushing files 5 stops... Show me a D800/5D3 comparison with the same exposure settings, similar lens, etc... Without being edited any. I have seen quite a few and the difference is barely noticeable, if at all.
Canon leads with better FPS, ergonomics, AF system, white balance, video integration, live-view, lens selection, high ISO and color/contrast SOOC.
That being said, the D800 is a great camera body. Chose whatever you think is best for what you shoot. Not exactly the same target audience between both cameras, so to me, I don't see how the decision can be so difficult.
Just out of curiosity, how is the MK 3's live view better than Nikon's implementation?