The kingmakers have now spoken. Stereoscopic 3D is out for video games. And in this business, whatever EA wants, EA gets. Just ask Sega and Visual Concepts.
I can't imagine Nintendo surrendering 3D just yet. They're heavily invested in the idea, and in fact, 3D is an obsession that goes back decades. They have always been convinced that a 3D display is the future of video games. Unfortunately, they've failed every time they tried it, whether it was Rad Racer on the NES, or the Virtual Boy, or the 3DS. Their hope was that the technology only needed to come around, and then the massive push by Hollywood towards 3D movies no doubt convinced Nintendo that era had finally arrived. Unfortunately, such an era has not arrived, and may never exist.
Does Nintendo have a contingency plan to remove the 3D display from their 3DS handheld? I would have to think they do, if they're sound businessmen. There has to be a Plan B. But I can't imagine they would pull the trigger anytime soon. As an admission of failure, it would be enormous, and the investments incurred to develop the 3D technology will be lost. It would be seen as a major retreat, and it would probably cost Satoru Iwata his job. But I think Iwata dooms himself and his company the longer he waits. When Sony enters the market with the PS Vita, Nintendo will be assaulted on two fronts (with iOS attacking from the other side). They lose "casual" gamers to $.99 iPod games, and they lose "hardcore" gamers to Sony.
How does a manufacturing company - and this is the kind of company Nintendo truly is - survive the transition into world without physical media? It's all going away, cartridges, discs, poof. The terrible irony is that it was Nintendo who proclaimed the coming changes five years ago. This is why they radically changed course with the DS and Wii. Unfortunately, as Nintendo raced back to the top, their old arrogant ways returned as well.
Again, I have no idea how Nintendo escapes from this trap, but I do know that sterescopic 3D and the Wii U tablet are doomed ventures. Eventually, the company must face that grim reality and deal with the consequences.