There are lots of factors here.
- our eyes usually focus and converge for the same distance; stereo has the convergence change while the focus distance (to screen) is constant
- the illusion of movement leads to inner-ear saying "no you're not" when your eyes think you are
- on the other hand, if you DO move, your viewpoint does NOT change (for stereo, it does for auto-stereo)
- we're only just beginning to understand production values in stereo (e.g. you can't cross-fade, don't switch camera rapidly, when switching be careful with the distance to the object of interest, be very careful with overlays like credits, and so on)
Obviously some of these can be dealt with under some circumstances, some not. It may well be that if your brain develops while being exposed to some of these, it will be much more accommodating. Exposure to stereo or auto-stereo might be good for children, who knows?