I don't go to movies, preferring to watch them at home. So, my perspective is for home viewing.
For the move from 2D to 3D, the closest audio comparison that comes to mind is the transition to surround sound. I'd put the switch from mono to stereo more in the same realm as the switch from black and white to color because it really didn't take any more planning on the users part. Surround sound, on the other hand, required placing speakers, setting speakers timings, and was really only optimal in one location. Oh, and when it first came out, it seemed to be used just to be used. It didn't follow the immersion approach described in that article. Years later, however, I think that surround sound is effective and isn't just gimmicky like it used to be. A lot of shows use it effectively to add an immersive element to the experience. Plus, electronics these days make is a lot easier to get a better audio experience in multiple locations within the viewing/listening area.
So, I think the things holding 3D back (kind of gimmicky, requires new equipment, requires glasses, not optimal in all viewing locations, and people aren't used to it) can be overcome. Will they be? I don't know.