...why do people think that the stereo 3D effect is all about popups? it's not. it's depth. and by the time you get used to the 3D effect, it becomes subtle and not as intense as before. why? because your eyes are getting used to focusing on a more distant point, and not on the surface of the screen.
it's actually a good thing when you get to this point, because that means your eyes are no longer straining to focus on what you're looking at. you see what you wanna see clearly in an instant, and it feels natural now. i know that this is good because i recently acquired a PSP, and by god the pixels on that thing is TINY! i almost always had to squint to see, but i can't pull the PSP too close else i lose focus entirely. so trying to see small stuff on something so close is just too tiring for me, and i almost always end up having to take a nap after only two hours or so. it gets that tiring.
now, the only reason why i'm not a big fan of popups much is because i can't quite see it, being far-sighted (i have trouble focusing both eyes on nearby or in-your-face objects). so the depth for me feels more natural because of that. but bottomline is, stereo 3D is all about the depth.
however, i do understand that for some, they like that "wow" factor and enjoy it a lot, so maybe a shoutout to Nintendo to up the 3D range for everything else that they decide to put on it, like maybe up the layers or something. from what i can remember off the 3D adjustment (look under Settings), the 3DS top screen can do something like from 3 to maybe 5 layers of popup, and something like 10 layers of depth. i didn't really count, but you can by counting the boxes on the side that stretches outwards as you adjust the slider.
EDIT: i never really answered the main topic, but here it is. how long before the "wow effect" vanishes? if you're talking about the initial intensity of the 3D, it's instantaneous for me. the moment i turn the 3D slider up, my eyes adjust instantly, even at max. now if "wow effect" means the immersion you feel when viewing stereo 3D, then it NEVER FADES FOR ME. i always feel it, however subtly.