Since I "upgraded" from a D700 to a D800 the only time I use M is panos and exposures over 1 sec. The rest of the time I use aperture priority and auto ISO
I do switch the focus setting but once you get used to the controls it is not a problem
I might lose 1 in 100 shots due to forgetting to switch the focus setting
I have lost no shots due to incorrect exposure
different people, different preferences.
the fact that you only use M for panos and long exposures, does not mean that everybody uses it that way.
my two user settings have more than one difference between them; I use spot metering when shooting in the dark because I need my subject to be correctly exposed and not the dark surroundings. so to start off I have one user setting that has high iso, spot metering, AE-L/AF-L remapped to AF-ON, and JPG setting to monochrome, because with dark shots it's easier to see your composition in b/w when reviewing it on the screen. the second user setting is more for general use: low iso, grid metering, AF with shutter button, and colour JPG setting.
the JPG settings are only for the image review on camera. I do not save my images on JPG but the embedded preview follows the JPG settings. I solely shoot on RAW, and this is also why bigger file sizes might matter: it takes up more room on your computer and your memory cards. you will also need the fastest and most expensive memory cards or else your buffer will fill up too soon, while trying to write the big files to the card.
it rarely happens that I need to shoot so many pictures so soon after each other, but it has happened at certain live concerts for me.
and talking about live concerts, this is where the M setting might come in handy: your camera can easily be thrown off by the quickly changing lights. if you set your camera to a static setting, your photos will also display the atmosphere of the gig better if some shots are under or over exposed because of it. the best photo is not always a "correctly exposed shot" (according to the histogram).
and these are only a couple of reasons why user-settings are handy and, for me, a must-have on any camera that I own.
and about the position of the focussing points:
as a test to see if I wasn't over-reacting, today I exported a lot of my recent photos from Lightroom using an overlay of the D600 focus points, and more than 50% of my focus areas fell outside the grid offered by the D600, but would have been covered by those of the D7000 or D800. so I might even have been under-reacting (if that's even a word).
I also went to the shop today to compare the ergonomics of both cameras, I discovered that for my hands and use I prefer the shape of the D800 grip (more rounded, less edgy), but that I prefer the D600's front left corner edge (where the camera rests on the ball of my hand, while I use that same hand for lens adjustments).
and even though the D800 is build more like a pro camera, more solid, I thought that the height and the weight of the camera were just a bit too much for me, and preferred the over-all ergonomics of the D600. all buttons are where I want them to be, and the lack of an AF-ON button is no issue, because in one of my user settings I have remapped the AE-L/AF-L button to do just that.
so my conclusion is that with a slightly more rounded grip (minor problem) and with a wider focus point area (big issue), the D600 would have been thé perfect camera for me. now it isn't.
as I said before: different people, different preferences.
if that wasn't the case, then we wouldn't need any different camera models at all.