Your complaints are certainly not uncommon, but the majority of people do not experience significant negative side effects watching active shutter or polarized 3D (Anaglyph works best with black and white images for shorter durations--i.e. comic book reading.). Your experience is abnormal. If you haven't had a comprehensive eye exam by an ophthalmologist or optometrist in some time, you might consider doing so.
Your headaches and other side effects are possibly due to your eye anatomy. If the problem is weakness with your intrinsic eye muscles, those can be exercised and strengthened to relieve the symptoms. There are actual physical eye exercises that eye care specialists sometimes give out to patients with binocular vision issues. If there is another mechanical problem with your binocular vision, that may need to be evaluated by an ophthalmologist.
The "vergence-accommodation conflict" of virtual 3D is a big cause of eye strain. In real life binocular vision, humans simultaneously converge, using their extraocular muscles, and focus, using their intrinsic eye muscles, to bring an object of attention into clear view. Of course, in real life, these actions occur cooperatively because you always converge and focus in the same depth plane. In virtual 3D, this reflex is disturbed because we always focus on the display screen, while our eyes may be required to converge at different depth levels. For many individuals, this is not a problem. For others with weak muscles or undiagnosed vision problems, this is more of a challenge and can lead to symptoms.
Other food for thought about causes of eyestrain:
If you haven't watched any 3D since the release of Avatar
, you might give it a go on a 3DTV at an electronics store or at a friend's house in a shorter duration to reassess what you think about 3D, your binocular vision, and the severity of your symptoms.
From my fortunate and limited personal experience, 3D movies have never once caused discomfort for me, in theaters or at home. The first week that I purchased my 3DTV a couple of years ago, I got a mild headache after about 3 hours of playing a 3D PS3 game. It also had stronger depth and lower resolution and frame-rate than movies, adding additional strain. In watching/playing more content ("exercising" my eye muscles), I no longer get 3D-related headaches with video games.