lusr, that is extremely non intuitive for sure. Have you checked in Nikon addressed this in a later firmware release?
Looking at the manual you apparently don't have to half depress the shutter, just the exposure compensation button (which has an aperture symbol next to it), but other websites suggest you do have to. I'll look into it when I can see the camera in person in a few weeks.
I'm pretty sure that you don't have to touch shutter in manual mode. I have d5100 so I can make sure in the evening if you want confirmation.
Why do this in manual mode?
Why not? Every pre-digital photographer did manual exposures. It teaches you to pay attention to your environment, and ultimately, I believe, makes you a better photographer because it develops your intuition about a given scene and what does and doesn't work.
I started off with P&S cameras and before I knew the mechanics of cameras I was frustrated with the automatic exposures; once I discovered I was missing "manual mode" I never turned back.
Sure, from time to time I'll use the priority or program modes when the shot is more important than the learning experience, but after 4 years of hobbyist photography I still find myself with much to learn and I enjoy the challenge of manual exposures.
I started out with manual everything cameras processing my own film, and I got pretty darn good a judging lighting by eye. Unless what you're trying to learn to do is become a human light meter, the "education" you're describing is pretty silly. You can accomplish the same results more quickly using the correct automatic setting and exposure compensation.
My D7000 is more straightforward since it has a separate dial for this and no need to half depress the shutter release. (I assume you can also change the settings using the LCD, but that's of no use if you're looking through the viewfinder and trying to set manual exposure.)