The problem with using 3-D for feature-length films is not so much the technology or its lack of contribution to the storytelling, it’s that human eyes were not designed to focus and converge on images at two different distances. Walter Murch, the legendary sound designer and editor, explains in a note to Roger Ebert:
The biggest problem with 3D, though, is the “convergence/focus” issue. A couple of the other issues — darkness and “smallness” — are at least theoretically solvable. But the deeper problem is that the audience must focus their eyes at the plane of the screen — say it is 80 feet away. This is constant no matter what.
But their eyes must converge at perhaps 10 feet away, then 60 feet, then 120 feet, and so on, depending on what the illusion is. So 3D films require us to focus at one distance and converge at another. And 600 million years of evolution has never presented this problem before. All living things with eyes have always focussed and converged at the same point.