There simply are intrinsic problems with stereoscopic 3D. The first is that the point of the technology is to increase realism. When you are experiencing that increase realism, 3D enhances the experience.
The problem is that because of the geometry of stereoscopy, 3D in a theatre only increases realism if you are sitting in a rather small sweet spot in the middle of the house; in a home, only if you're sitting on one properly placed piece of furniture. Sit farther back, and depth is exaggerated. Sit farther forward, and it's flattened. Sit to the size, and everything is skewed--cubes become rhomboids. Instead of being more realistic than flat cinema, it becomes less realistic.
This Cabinet-of-Dr.-Caligari effect is novel and stimulating, but it is not realistic or story-enhancing. It's rather like the early days of color TV. Colored snow, and actors changing from purplish to greenish as they walk across the screen, have a gee-whiz appeal, but in the long haul it has to be accurate or it doesn't satisfy, and it can't be accurate if they want to fill a theatre.
A second problem is that 3D doesn't really work unless the picture is so big that you are never looking close to the screen edges, where you get insoluble problems with binocular disparity if any object in the screen image is closer than the physical screen.
The second is that you only get an increase in realism if the director and cinematographer throw out a century of screen grammar, and limit themselves to using lens of one focal length. And, the more realistic the basic process, the more jarring something as ordinary as a cut is. We've learned to take cuts from a long shot to a closeup in stride, but it's harder if the image is so realistic that every cut induces a sense of physical movement. The re-thinking of how to tell a story on the screen might be possible. After all, the introduction of sound posed similar problems in the early days. But adding sound meant adding a whole new sensory modality. 3D is really, at heart, just a better picture... just like Cinerama or 48 fps Showscan, neither of which had staying power despite being a breakthrough in realism.