OK, now I know 3D is a hot topic these days, but it isn't going to be damaging our brains any time soon. If you have not noticed most of us see things in 3D every day, and we are fine. We see 2 2D images within a 3D space which we splice together in our heads as one coherent image. Same with this 3D tech, we are seeing 2 2D images that we splice together, it is nothing new, and nothing unnatural about the general idea of this tech.
Close up I could see a problem, but it is not with 3D, it is with people with weak eyes who already have trouble with close up images, who are trying to strain to distinguish depth within a field they already have issues with.
Another potential problem is with the depth of field being different than what we are accustomed to. Every person has a different perception of depth due to the spacing of their eyes. In theory those with wider set eyes could have a less exaggerated (and perhaps more accurate?) perception of depth, while those who have close set eyes would have an opposite perception. But lets say that you have wide set eyes, and the movie is captured with lenses closer together than you are accustomed to (or the display is calibrated that way) then it would be jarring and disorienting. Sure you would adjust with time, but it could be annoying.
I went to see Avatar about 7 times at different theaters, mostly because I knew my living room wont have anything that mind blowing in the next 10 years, and also to see how the movie differed from theater to theater. And let me tell you, there were huge differences depending on where you were. Some theaters greatly exaggerated the depth of field (the images being too close together making things look deeper and skinnier than they would be in real life). Other theaters had a shallow depth of field, which I found much easier to watch, and less disorienting after leaving. One theater here in Ohio was fairly close on the depth being right, but they had a dirty spliter so there was bleed over between the 2 images which did some strange things. Now playing with how our brains see depth may cause temporary issues, but it wont be anything long term.
It reminds me of a college that used special glasses on some test subjects that made everything look upside down (we actually see upside down to begin with and our brain adjusts for this), and after a few days their brains figured out the new rules of how to process what information was being given and they were able to function normally, even playing sports. Removing the glasses after the test screwed them up again for a while, but they eventually went back to normal. If the human brain can adjust for that then I am sure a little 3D wont hurt anyone. The gimmicky and crappy shows that implement it may keep you living in your trailer park... but aside from that no harm done.