It's more like "3D" has a problem than just "3DS" has a problem.
The 3d market is hard to buy into with a lot of the recent negative media behind it. People have been told their kids can't see it as it might permanently damage their vision. I mean, after hearing that, who would ever want to buy a 3d product? This is sort of Nintendo's fault since they were the first to put out this information. I realize they are trying to avoid lawsuits but come on. They've likely shot themselves in the foot and they will still get lawsuits anyways (there is never an end to the amount of sue-happy people wanting to make a quick buck).
Plus there has been lots of spinning about headaches and sickness. Anyone who has actually played it knows this is overblown.
