The latest Iwata Asks explains how the 3DS hardware's distinctive layered look was inspired by a number of practical considerations.
The 3DS looks like a particularly delicious cake as a result of an intention to aid accessibility. Rather than carve an indentation into the top layer, or add an easily-damaged catch, Nintendo engineers gave the upper face an overlapping rim.
The second layer, which plays host to all the console's external switches, has been recessed, and this in combination with the over-size upper face, protects against accidental activation while playing or in your pocket.
The third layer is a nice clean canvas for labels and LEDs attached to controls on the layer above.
Apparently, the different colouring of the three layers represents the constant content updates of Street and Spot Pass. That probably makes more sense in Japanese.
During the discussion, it was revealed that Nintendo went through at least twenty prototypes, and that developers requested numerous changes to the Circle Pad, which was only set in stone after E3 last year.