Some of us are old enough to remember the audio industry's brief and unsuccessful flirtation with four channel "quadraphonic" sound. With speakers arranged at four corners of the room, it could sound reasonably convincing, provided the listener sat in the center of the sound field and kept his head absolutely still. If you turned your head, the sound source had a tendency to "ping" from one location to another. It was a technology that was supposed to deliver surround sound; unfortunately it appeared to have been created by people who knew everything about audio electronics, but nothing about how people actually hear.
Similarly, 3D movie technologies appear to have been created by people who know everything about digital projection, but nothing about how people see. In fact, "3D" is a misnomer: what you're actually getting is "stereoscopy", like a Magic Eye picture or (if you're older) a View-Master. Consequently, the picture only truly looks "right" from one position, where the relative positions of the stereo images "make sense".
In reality, stereo image separation is only one cue of many that people use to infer depth, and most of the cues we rely on are already present in a 2D projection. If they weren't, we wouldn't be able to make sense of flat images such as photographs and paintings. We would perceive them merely as lines and blobs of color rather than as representations of the world. (This is especially true of images rendered on a surface whose geometry actually contradicts the image, for example a Greek soldier painted on the side of a vase.) Conversely, if stereoscopy were so critical to depth perception, there wouldn't be so many animals that sacrifice binocular vision for enhanced peripheral vision by having their eyes on the sides of their head.
The biggest problem with stereoscopy in the movies comes when the stereo cue is inconsistent with the many other cues such as motion parallax, depth of focus, or relative motion (unless you're sitting in the theater's sweet spot), as it often is with 3D movies. What you then get is a headache or, if you're really unlucky, motion sickness.