The only problem I see is there won't be as much action going on on the bottom screen, if any at all. All of the game's action will occur in the top screen, while the bottom screen will be mainly utilzed as another form of control for the player, a touh panel.
There's a video (I don't remember where) of Nintendogs and Cats where the player can interact with the dog using the touch panel. The dog is displayed on the top screen, but there is a silhouette of the dog on the bottom screen. so interacting with the silhouette dog directly affects the dog on the top screen. I don't see any issues with this, and I imagine other games will work in a similar fashion. I can see something like a pointer apperaing on the top screen when using the touch panel.
There really isn't any need for both screens to have action, especially considering the top screen will have 3D. Don't expect any action to hop onto the bottom screen.
