The whole idea of 3D on the 3DS is fundamentally flawed. Ignoring for a moment the obvious issues of some people not being able to see 3D, eye strain, etc. it's 3D that only works if you're looking at the system from a very specific angle. Which, since it's a handheld, is almost never. Not to mention I've yet to play a single game on it where 3D added to the gameplay experience. Even things it should help with like judging depth for jumps in Mario, it didn't help at all compared to the 2D.
So basically, it's a gimmick which doesn't really improve your gaming experience, and which will constantly have you adjusting the handheld because the screen is a few millimeters off the sweet spot. Utterly useless, and a shame that it was in there raising the price for so long, and the only option people have for skipping the 3D and saving some money is the atrociously styled and less practical 2DS.