I came across a pretty interesting article the other day about why 3D movies give some people headaches and some of the technical issues with “faking out” your eyes and brain.

Article:  Why 3D doesn’t work and never will. Case closed.

One of the biggest issues, as this article states, is the focus/convergence issue.  When you focus on things, not only do each of your eyes lenses focus, but your eyes also converge and diverge (rotate toward and away from each other).