Yeah, below could be good, but since the Wii U has it above, I thought that would be the new style in a way that people would get used to for nintendo games. It would be tricky to switch back and forth between the two styles.
For the people that say the second circle pad "isn't needed" because there aren't that many games, I disagree. Sure it isn't "completely necessary", but the added functionality is a valid thing. The opportunity for developers to use it is a valid thing. For example Kid Icarus Uprising comes with that stand to hold it in place because it is very difficult to stay in the 3D sweet spot when you are controlling the camera with the stylus. I think that shows partly why a second circle pad would be particularly good for the 3DS. It would be easier to control, I think, and stay in the 3D sweet spot.
Don't get me wrong here, I love it all the same and will no doubt be getting one at launch, but I just had my heart set on the second circle pad!
I will also be willing to bet that Nintendo tried out the design with the second circle pad and decided against it for some functional reason, but I am not sure why. But I am willing to give them the benefit of the doubt.