I think one of the main issues with 3D is that you are forced to focus on what the director intended you to focus on. This is not true in 2D, you can focus your eyes on a blurry area over the characters shoulder without a problem. It will be blurry but your eyes can focus on it. In 3D, your eyes try to bring that unfocused bit into focus like they can in regular 3D space and that's what causes the headaches/vertigo/eye strain.