M9 can't autofocus, because it's a manual rangefinder.
M9 can't autoselect aperture, because it's compatible with every M mount and M39 lens ever.
M9 can't do multiple exposures in camera.
M9 can't do PHOTO EDITING and ART EFFECTS in camera.
M9 doesn't have a bajillion useless menus (who the fuck would use a different type of beep. REALLY).
M9 is 1/4 - 1/3 the size.
M9 has more pixels than the S and not many less than the X, which is pretty remarkable for the body size.
M9 has no AA filter so you can get sharper results, though you do need to PP a bit.