Basically, in some of the Iwata Asks segments about the 3DS, they talk about how 3D gaming made a few things a bit difficult due to lack of stereoscopic vision. One of the examples they used was flying through the rings in Starfox, while the one more relevant to me was jumping on the stomps in Mario. Considering how annoying that first world was on Mario 64 in terms of getting the star by getting Chomp to break the cage, I would agree with them on that count.
Basically, it adds to gaming what most people have in real life but not when staring at pictures, stereoscopic vision, so you can judge the distance between your game character and whatever thing its trying to jump onto, hit, run to and so on much better than you would if you were just relying on monocular depth cues such as shading.
Here's a nice read between monocular and binocular depth cues. If what I've heard is right, your basically having stereopsis added.
Hey, just because you can't understand how it would work doesn't mean they didn't do it, considering they actually had the entire conference hall play the 3DS to judge for themselves.