Yeah, I agree -- it's Nintendo's job to try to make 3D with glasses feel obsolete, so they're not helping their competition, while it's Sony's job (and all the other companies who have a stake in 3DTVs, movies, and console games, as you said) to show that the experiences are fundamentally different. This is a battle which will be fought (and it seems to be starting right now). But I suspect Nintendo will be better at leading with what they do, rather than what they say.
One of the most interesting things to me in Nintendo's conference was hearing Miyamoto (or was it Iwata?) saying that 3D really changes the gameplay experience in a three dimensional world. When Nintendo starts talking like that, I'm on board immediately, in fact I get a little choked up, because I believe what they're saying isn't just marketing speak. But the problem is, their arguments for the beauty of 3D gaming actually help the competition, and they have to try to counteract that at every turn with the glasses caveat. They're kind of having to fight against their own brilliance in what they're doing, which is one of the reasons I suspect the argument won't be enirely sucessful.
Then again, I'm saying this as someone who intends to own 2 3DS pretty early on (my girlfriend wants one) and probably will never get into 3DTV tech, but that's really because of the prices involved -- I don't intend to buy a new TV for many years (hopefully) and paying more than ten dollars for the glasses is a hard sell to me.
