After finally spending some good time with it, I have an idea of what I would have preferred.
The clamshell design is nice, but I would give this up in a second for a larger wide touch screen similar to that of the PSP. The current screens feel rather small to me and the view angle is very poor. The tilt from the shell design generally means that one screen will look better than the other due to the viewing angle. Simply shifting your hands a bit can impact your view greatly. Also, the size of the two screens is roughly equal to the size of one PSP screen. Why not use one screen and make it entirely touch based? Would be neat. The screens are my biggest complaint.
I would prefer a more rounded design with a thicker base. I spent some time with a couple GBA games as well, and I found that my hands hurt afterwards due to the thin base and square corners. I could not get a real grip on the machine. I think the face buttons should also be larger.
I would also like an update to the main UI. It seems that adjusting or using just about anything requires a reboot of the machine. I do not understand why, but it really damages the feeling of a cohesive environment.
It's a shame they didn't take a look at the PowerVR mobile solutions. As much as I enjoy disagreeing with Lazy, I do think that the PVR sounds fantastic on the mobile front. Of course, I do not know if it would have been possible (costs, availability, etc.).
I think it would have been best if they could combine the strengths of the DS and PSP hardware into one unit.
If nothing else, I would have preferred Nintendo to use much higher quality screens. I would have gladly shelled out an additional $50 for brighter, higher resolution screens with a great viewing angle.