Actually, I've found just the opposite. After twenty years with my OM-10, I confidently expected MF to get me more accurate focus when I first got my XT, but side-by-side comparisons and testing led me to believe that the AF was actually
more accurate by a hair or three.
I blame the matte focus screen. It makes it far more difficult to accurately judge tack-sharp focus than the old split-circle focus screens. And mastering your autofocus points will take care of the major issue of having the camera focus where you want.
If you want the higher accuracy of manual focus from the old film days (especially for narrow DoF photography like macro shooting), you may need to swap out the focus screen for one with aids to help you achieve pinpoint accuracy. The Katzeye, and the Haoda are the best-known third-party suppliers of these screens; but Nikon and Canon do make swappable focus screens (usually for the higher end camera bodies) that can help, too.
With macro photography, though, I tend to find that I'm focusing not with the camera's focus system but by varying my distance from the subject: I do this tiny little rocking back and forth.
