Love your avatar. Monster, by Naoki Urasawa, right? I've never read the manga nor seen the anime, but have heard good things from it. I have finished 20th Century Boys though, even seen the movies.
Anyways, obviously building up resistance isn't at the cost of losing something else. Nobody in their right mind would take it that far.
What I was talking about was, for normal people with relatively normal eye conditions, a little bit of vertigo or lightheadedness after the first few minutes of intense stereo 3D immersion is natural, and continued exposure to it would make you get used to it to the point that super strong 3D will just look weird for you but not disorienting.