I have both the D800 (not the E) and the M9. IMO the D800 is a much better camera (broad term) in many ways. The raw files are easy to work with and very smooth, much broader dynamic range, very clean high ISO, deadly accurate autofocus and on and on. I'm sure you've read others comments and know all about it. By comparison the M9 is stone age. I do like the look of a CCD vs CMOS. I know the arguments but every CCD camera I've owned, 1D Canon, Hasselblad digital camera and the M9 have a look. I believe the color is more true in the CCd cameras. It may just be processing but all three cameras share a common look.
The big deal about the M9 IMO are the lenses. I bought the D800 to use in my documentary work where I shoot under very poor and low light. I often must shoot at high ISO and wide open or near wide open. The Nikon G series glass which is their best at the moment just won't cut it wide open. Corners and edges stink and are pretty much unusable. I purchased thee Zeiss ZF 2 lenses, 25 f2, 35 f2 and 100 f2. They were no better wide open and wound up sending them back to B&H. At this point I figured the only choice was to bite the bullet and get an M9 and some new asph glass. I wound up with a new 24 Elmar, 35 Summilux FLE and 50 asph Summilux plus my old 75 Summlux and 90 Apo ASph Summicron. Like I said it's all about the glass. Stopping down to f8 to get sharp corners isn't an option for my work, the lens must be sharp corner to corner wide open. The 24, 35, and 90 are just that sharp wide open even in the extreme corners. I can actually shoot wide open and not get mush at the edges and corners.
I do really like my M9. It's stone age but I knew that in the beginning. I bought it for what it is not how it compares to any other camera. It's unique and the correct tool for my kind of documentary work. No one has lenses that perform like the new generation of Leica glass. After forty five plus years of using Leica M's it feels and operates like an old friend. I don't even mind the noise at high ISO. High speed film has grain and that enhances the mood of my work. I don't even find the sound objectionable.
It kind of purrs I guess.
I do also love my D800 and would not give it up. Both combined along with my Hasselblad make a superb system. One is no better than the other. they are simply different tools for different jobs.