The biggest reason the 3DS can't provide what feels like a hologram is that the screen is too small. As objects come closer, they need to get bigger, but they can't get bigger than the screen's dimensions. So most games focused on objects going into the screen, instead of popping out.

But I think the 3D served one really wonderful purpose: it made the small screen feel larger overall. Not large, maybe, but larger than it really was.