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I agree that Nikon's live-view implementation is not ideal. This is more obvious when you compare it to a dedicated live-view camera like a Sony NEX. I wouldn't mind it so much if OEM screens were available to swap in for accurate manual focus of fast lenses.
For now I just set my aperture to wide open, engage live-view to focus on my D600, magnify, achieve focus at 100% with the zoomed in box, disengage live-view, set my desired shooting aperture, confirm composition through the viewfinder, and shoot.
On my NEX-6 I tilt the LCD up, focus at my desired aperture under one-touch 100% magnification, one-touch zoom out to full view, confirm composition, and shoot. LCD will brighten enough to give details for successful focus, and can be set to a "torch mode" for shooting outdoors in bright light. Alternatively, I can do everything through the EVF.
Those are my processes when on a tripod. I shoot exactly the same with the NEX handheld using either the LCD or EVF. With the D600, I get it close with my eyeball through the OVF, then rely on the rangefinder dot, and hope for the best. Live-view is arduous at best handheld. My hit rate is essentially 100% with the NEX, and about 50% critical focus wide open on the D600. When I stop down, I'm closer to 100% with the D600 of course.
The Nikon DSLR bodies are excellent for so many types of shooting and are ergonomically superior, but are lacking for manual focus glass usage compared to other cameras. I plan to try out one of the rumored new full-frame NEX cameras when they are released.