I don't see many 3D vision PC gamers complaining and we spend many many hours in front of 3D content (basically 90% of PC games are compatible and work really well)
However the article does have a point, there is a slight adaptation time for higher settings of depth (cinema should be set with a moderate depth). On 3D vision, there is a depth wheel.... you can't play on higher levels at first cause you just get crosseyed, but once you're used to it, then you can increase depth.
Also the "like a new pair of glasses" part is probably correct, it does make you addapt your vision.
Games have the adventage however that the depth is not necessarely out of focus... so the discomfort might be lessened.
On a side note... coments on the 3DS are absurd... that 3D does not make your eyes work at all... (provided it is indeed the polarized screen tech they will use =) ).
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