I think Miyamoto mentioned that he liked the multicolored Super Famicom layout, but NOA went with the purple design instead. I'll always remember being a kid and seeing the Super Famicom in Nintendo Power before the US SNES design was shown and thinking that design with the multi-colored buttons was neat.

Which do you prefer, a hypothetical Super Nintendo that looked like this:

Versus

Note I think the purple SNES design was the only one with the concave (like NES) + convex butons (like N64) for the Y/X and B/A buttons.  

NES  >   Famicom

SNES <  Super Famicom

"Hypothetical"? We had the Super Nintendo in Super Famicom form . Anyway yeah I think you in America got the short end of the stick, the shape of our/the Japanese console is better, as well as the cartridges and the colors of the facebuttons instead of the purple.

I prefer the EU/JP console. Get that Purple outta here.

It's weird because in some lighting the purple Super NES (especially a crisp/clean SNES) seems to look better:

Nope I still prefer the one on the right. :P

I always wondered, why was the design different?

I prefer the JP/PAL version but then I grew up with it so the other one is just weird. I mean the controller looks like a cheaper knockoff because of the button colours.

Nintendo of America did not like the bright colors and design of the SFC apparently so they redesigned it. 

For good measure, here is a prototype Super Famicom unit from 1989 or thereabouts:

I think this might actually look better than both the SNES (purple) and SFC. 

When I first saw the US version of it I was actually quite shocked. It's probably the ugliest console ever built.