Heh, I was just talking to ruby about this. When they first showed the NRC, I thought of putting the D-Pad to the bottom and at the top having an SNES diamond-style button layout. I think he made a concept of it.
Anyway, there are a few problems with it. First, it takes away the potential for one handed gaming. With the D-pad at the top, it would be easy to have some games implement it, but with it at the bottom, it wouldn't be able to happen. I don't see this as a big problem, but someone else pointed it out earlier.
Another problem, though, is the nongamer one. Sure, there's only one more button if you go with a diamond layout at the top (since in the current setup there are two small a-b buttons), but if the diamond layout is chosen, it would basically be a current gen controller split up and with motion sensing added. Nintendo has constantly stated that they think too many buttons will alienate nongamers, and that the current controllers do. It's worth mentioning that Nintendo certainly thought of the implications when they put only one button on top. In fact, in one of their concept booklets, they have a big A button with four kidney buttons surrounding it. However, they chose not to go with this, and I can understand why.
The last problem I can think of is that using many button combinations while also utilising the motion control has the potential to be very confusing. The one A button is simple and will not cause confusion. Of course, if more buttons were added, it wouldn't be a problem with Nintendo games, as they could only use one of the buttons. This isn't the case with third-party games, though. Even if they have a brilliant way of using the motion control, they may add button combinations that would get in the way, and the result would be very awkward controls.