First is that the technology is just plain uncomfortable. The glasses feel bad, and my eyes hurt after a while.
Second is that filmmakers seem to have no clue how stereoscopic depth perception actually works. Objects only have perceptible parallax out to a couple dozen feet. Beyond that, depth is perceived purely by other means. But 3D movies keep applying parallax to objects much farther away. All this does is make them look closer and therefore smaller. The worst example I saw of this was an IMAX film at the Smithsonian about the development of the Boeing 777. There was a scene of a distant 777 in flight which popped the plane out of the screen. The result was that this 100-ton building-sized machine looked like a child's toy.
If the technology can be improved so it doesn't hurt, and if filmmakers can figure out how to use it without it looking utterly stupid, I'll give it another shot. Until then, I'm sticking with 2D.
I generally am not a fan of 3D, but my theatre seems to light 3D movies perfectly, while their 2D showings often seem dark.
When it's badly done it makes my eyes hurt after a while and I find it tends to make everything look blurry
Perhaps a broader reason is that 3d seems to encourage filmmakers to go for visual spectacle over good storytelling.
She loved the experience, so I sat there for three hours watching a blurry movie because the 3D glasses were awful and causing pain.
Never again.
I can certainly see how too much early exposure would actually interfere with the development of the usual association of cues that support perception of distance.