It's probably that some "well intentioned" kid cranked up the 3D effect all the way up on all machines... that'll give you a headache for sure..... if you can even see a 3D effect that is.
I seriously doubt there was a significantly high rate of discomfort to players when Nintendo tested the device....
Though yeah there is eye discomfort with 3D... I my self have my eyes stinging a bit after a 6 hour session yesterday with a moderate setting.... well maybe it's due to lack of sleep too as that lasted 4 hours... :p
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