The brain is very good at rewiring itself to accommodate novel visual effects. The problem is that it might adapt too well, and not adapt back fast enough afterward. Like when driving the car after a long 3D TV session. If this affected only 1 in 1000 people that's still big lawsuits. I think 3D is dead.
When I watched Avatar 3D I noticed some eye strain which will probably be different per person. My 6 year old nephew was sitting next to me he reacted to a couple of early scenes but when the golf ball rolled out he went to sleep soon after. I felt the visual cues that we require in everyday life were missing. Much like trying to fly an airplane under the hood its disorienting. When you see some thing coming in 3D coming at you your reflexes want to move but you tell yourself its only a movie and you don't need to move. I think the brain will adapt. Plus I had little or no disorietation after the movie.
As a stereo photographer I have learned to tolerate the vergence-accommodate disparity, because that is the only way to "free view" side-by-side left-and-right images on stereographic cards without the need for glasses. You just stare off into the distance so that your eyes diverge, then slip the stereo card up into view until your eyes accommodate a close focus. Vergence is distant, but accommodation is close, a combination that is not normal--a disparity--but it can also be an acquired skill. In our stereo camera club (disclaimer: I am tech editor of the non-profit club newsletter, Stereo Views, and run the Uptown3D.org web site), about half the members have learned to tolerate this disparity and "free view" stereo cards without glasses--but the other half complain of discomfort and give up. I suspect the same will be true for 3D TV. For some it will be a joy, and the others will just flip the from 3D-to-2D.