Here's the thing:
The 3D is not quite as people think of it. When most people think of 3D, they think of hands popping out at them, things coming through the screen and the like. That could be happening with the 3DS, but here's the 3D effect's main purpose:
"In the past 3D Mario games, and 3D Zelda games for that matter, if there were several floors at the same height, it was hard for the players to tell if each one of them was located with the same distance between them, or if just one was further away and higher than the other floors. On Nintendo 3DS, you can readily understand the height and distance of the next floor in front of you. You can feel the difference by switching between the 2D and 3D modes. You might have had a hard time trying to jump on a stump or to hit a floating question-mark block in 3D Mario [games] until now, but you will be able to do so easily on Nintendo 3DS." - Shigeru Miyamoto
It's not to be all gimmicky with the "out of the screen" idea. It's to show depth, and the people who are just watching don't really need to see that. It's there for the assistance of the gamer, not someone who's watching.