I think it is smart to have different sized screens. It allows us to have a bigger screen for gameplay, but also the size of the system doesn't change.
Also the touchscreen is good for an input device, but not always good for gameplay, specially if you are touching it at the same time, or having to look at both screens.
The different sized screens don't really matter except for when the action switches between them. Games like Contra 4 wouldn't work unless the sides of the top screen were blacked out. By this, I'm not referring to backward compatibility. Rather, a game that uses both screens as one big screen. If that's the only real difference, I can't see Nintendo justifying this design choice. Everything that can be done with the current 3DS set-up is possible with 2 widescreen displays. For games that need the whole screen for gameplay, there's the top screen. However, some of the most innovative software on DS such as Elite Beat Agents, Nintendogs, and The World Ends with You used the touch screen as the main screen for control and gameplay.
But it looks like there is enough room for the wide screen on the bottom without even moving the analog, dpad or buttons.
Pretty sure there is, however, the point is moot, considering these are prototypes which may reflect the final design, but are prototypes nonetheless. If there isn't room, Nintendo has like 8-9 months to come up with a different design. Nintendo did it in less time 6 years ago.
And I'm with you on the real-estate of the top screen. It's due to the bezel and placement of start/home/select which could be easily moved.