You know how you have the ice cream part that goes in the middle and the cookie parts that stick out? The 3DS is designed like that, but for a very good reason.
The original DS was pretty easy to open and close. The DS Lite, however, was not. When shut, it clammed up. And worse yet, it was a fingerprint magnet.
The 3DS was designed not to be a fingerprint magnet. That doesn't mean players won't leave a set of prints, they will. But the coating will enable them to wipe them right off.
The DS Lite design looks sharp - especially closed - but with the 3DS, the thinking was very much function over form, hence the layered look.
The top layer juts out, making it easy to open. The second layer, Nintendo says, contains the volume slider, separating it from the other layers. The button layer, then, also sticks out slightly to separate it from the other layers.
The layered look gives the Nintendo 3DS a unique appearance, different from the previous systems. But does "different" mean "better looking"?