Maybe I'm just in the minority, but I have never had a problem with 3D, and I've seen all kinds of 3D - red/blue anaglyph, green/yellow anaglyph, active-shutter, polarized, lenticular. I've never had eye strain. My wife, on the other hand, gets a headache with red/blue anaglyph but not with any other form of 3D. None of my three kids have ever reported eye strain after watching a 3D movie in the theaters. My only problem with 3D right now is that my TV is only three years old and I can't justify buying a new 3D TV! I want my 3D gaming!
I understand that some people do have problems with 3D; but I wonder if the problem is with the technology, the way that the technology is implemented (insufficient brightness), if it's possible psychosomatic, or a combination of the three.