Because stereoscopic images are not 3D.

When looking at several objects placed at different distances in real life, your eyes will change focus from object to object.  But with stereoscopic "3D", the focal plane remains constant whether or not the magic mushroom is "near" or "far."

The flat focal plane of stereoscopic images is not natural and can even mess with a child's developement of functional depth perception.

http://zcint.co.uk/article/sega-covered-up-vr-headset-health-risks

I tried one out and it was fine when I looked at it dead on, then I moved my head 2 centimeters to the left...

i cant stand the 3d on any setting, it doesnt really hurt my eyes its more like its a distraction from the game.

It's just a really nice tool for certain games but if you are considering buying a 3ds you should know there is an option in the system settings to disable 3d entirely on the console, this disables the slider even on the home menu, I did it not for lack of seeing the 3d effect but I played the majority of 5 shiny staring Mario 3d land in full 3d and my god that game looks amazing, nothing compares to feeling almost scared that bowsers rolling fireballs are going to shoot outta the screen and hit you BUT back to what I was saying, you need to hold it fairly still for the 3d to stay in perfect focus and doing this for 20+ hours of game absolutely gave me really bad neck cramps when I came away from the game, just had tensed up my neck too much to keep perfectly in focus while playing and yup strained it.

Should be worth noting btw, my missus has picked up a 3DSXL recently and the 3d effect on that is a whole lot easier to find the sweet spot/spots for and is far more forgiving on a little moving so if you really want 3d and you want to give your eyes a good break invest the extra money and XL it up. Orrrr do what I did, I believe it's in the parential settings of the system you just basically lock the 3d so kids can't use it and hurt their eyes while they develope, but it means whenever you press A on an App from the home menu (except old ds games and ambassador games) then you get 2 options pop up, A for 2d and B for 3d if you mash B you gotta tap in your 4 digit pw and you unlock 3d, if you dont want it just tap A again and you're away  in happy  2dland

my eyes get strained after about an hour if i have my XL on max.

I don't have one, but I played with my cousin's 3DS for over an hour, And i've got the same effects than you.. Felt like my eyes are going crossed. tought it's just cause it's my first time or me wearing glasses ..
Do you guys have no matter with it while you're wearing glasses ?

Judging it based on a store demo isn't a good idea, because it takes about a day or two of heavy play to really get used to the effect. That was the case with me anyway. Everyone's eyes take a little while to adjust to it.

Now it's not a problem at all. Really though if you don't like it, just turn it off. Simple as that.

Every current 3D system hurts my eyes, maybe it's because as a kid I was cross-eyed and it took me 11 years of corrective glasses, the first two or so with eye-patch too, to heal them.

I play all my 3DS games with the 3D on, i feel it enhances the experience, even if the game isnt really designed to use 3D features. It just makes them look prettier and add a bit of depth, after playing Zen pinball in 3D i dont think i could go back to playing 2D pinball games.

yeah for the people whos eyes perfectly can see the 3d effect it's as tho where the screen is simply fades away, it isn't like the adverts tho where it comes out from the screen up towards you, it is far more realistic to say that is more like looking into a deep box rather than looking at a flat screen, I could imagine that would feel absolutely perfect giving you a pinball table feeling.