You can get headaches for two reasons, eye strain from strange viewing, and fairly simply, from effectively shutting your eye on and off very quickly constantly, MANY people get headaches from it and its mostly for the second reason. There is no way to deal with it, if you get headaches its completely useless.
The thing is a tech will NEVER in a million years make it to the mainstream of support, if it induces physical sickness in people. IE< it will die like most other 3d incarnations before it and many more to come. Its not new, its very old, its pointless and having played several games on it, it add's almost nothing.
120hz screens being used at 120hz is a huge step for LCD's(maybe OLED's by the time its standard), killing that step up by running at 60hz effective is just soo soo pointless.
I'd kill for a half decent 120hz screen, I'm happy with TN but didn't like the ones available, would quite happily drop from a 24" to a well, I'd prefer a 20" over a 22" as they are shaper for the same def, but not to a completely crap 120hz screen.
Unfortunately I don't see there being many good quality 120hz screens till every manufacturer has a couple versions out.
Its quite possible people are waiting on OLED's before putting out their 120hz screens en masse, as they have a lot of advantages, and 120hz will be a pretty humongous step so by coupling it with OLED they basically have a superior product in every single way, which makes it easier to sell, especially if its a more expensive alternative which its likely to be.