I know I'm late to this thread, but I didn't see anybody else say this.
After my son had corrective surgery for a crossed eye, the surgeon warned us that artificial 3D would inhibit his development of real 3D. He was born with the crossed eye, so he never had stereoscopic vision. It took about 6 months after the surgery to get a bit of depth perception, and about 18 months before he could pass all of the 3D vision tests.
Once he passed all the vision tests, the doc said to avoid artificial 3D, because it could cause the eye to re-cross. Now he's at an in between age when a re-crossed eye could cause him to lose stereoscopic vision permanently. If it re-crossed, and was left untreated for long enough, there's a risk that his brain is flexible enough to drop the neural paths, but not retrain when stereoscopic vision is surgically restored. ie, a very small risk. At some point (16 I think?), he'll be old enough that it's not likely to happen anymore. Given the relative risk/reward of artificial 3D, it's not worth even the tiny probabilities involved.
Yes, there are technical work arounds (ThinkGeek sells some "2D" 3D glasses). If it was something useful, I'd do it, but artificial 3D isn't worth the effort.
Full disclosure: I don't like artificial 3D. I can see full 3D, and I'd still buy a 2DS over a 3DS.