Fortunately I don't get headaches from 3D (and I also have good enough vision to not need glasses- 20/25, thanks for asking), but it does irritate me to watch 3D for any real length of time. Why? Forced field of focus. In a 2D movie, my brain understands that I'm watching a flat image, and therefore something being out of focus doesn't bother me. But in 3D, if I instinctively try to focus on something that is not in focus in the shot, my eyes begin to strain in the attempt to shift my field of focus- only it can't, because the object itself is unfocused. It only tends to be an issue when the director decides that we absolutely have to focus on some object way in the foreground or background- but that seems to be a popular decision.
And why is this an issue? Well, go look at the trailer for the new Thor movie. What does it say at the end? "In 3D, and 2D in select theatres". More and more theatres are getting in on the 3D craze, and it's not at all a stretch of the imagination to see how 2D showings are going to start being difficult to get into. (Think about it from the theatre's perspective: One investment in the technology, then they can cash in on the popularity of 3D; plus it's not like 3D releases are nearly as widely pirated as 2D ones!) So it IS something to worry about for people who don't like the 3D technology, for whatever reason.
And why is this an issue? Well, go look at the trailer for the new Thor movie. What does it say at the end? "In 3D, and 2D in select theatres". More and more theatres are getting in on the 3D craze, and it's not at all a stretch of the imagination to see how 2D showings are going to start being difficult to get into. (Think about it from the theatre's perspective: One investment in the technology, then they can cash in on the popularity of 3D; plus it's not like 3D releases are nearly as widely pirated as 2D ones!) So it IS something to worry about for people who don't like the 3D technology, for whatever reason.