I don't understand why people are "upset" about this happening. You do realize it will have an off switch? It will be the same as adjusting your brightness. Not everyone wants a super bright screen, as does not everyone wants to view their device in 3D. There is a zero chance Apple releases a 3D product without the means of turning it off.
Adjusting the 3DS's 3D capabilities is a slider away. If you want to play your games in 2D, the way you've always done, you can still do this with ease. 3D is an additional feature for times you may want to use 3D on your device (watching Avatar on a plane). It doesn't mean you're going to be forced to use 3D while reading the New York Times.
I think what people are annoyed with is the constant discussion of 3D in mainstream media. It IS annoying, and I wish for it to stop, but at the same time, I can't find a reason why this technology would be bad for the iPad / iPhone, as it's being added on to the interface, rather than replacing it.