I would be somewhat annoyed if the Cafe didn't feature an improved pointer controller. Unless they can keep the Wii brand alive on the Cafe with Motion Plus Wiimote still selling at retail, and if the Wiimote Plus is forward compatible. If individual Cafe controllers are pricey I can see Nintendo considering such a plan. One machine, two different kinds of marketable control methods (casual/hardcore).
How much of this is based on research of DSiXL consumers? If they find that these users stay home, why not keep these sales in the home environment. The Project Cafe concepts reminds of the DSiXl, being a really interesting move towards making a handheld/home console hybrid. A safe and controlled household network for entertainment is a great idea, especially for large families.
This makes me question if whether the Project Cafe could push information and gameplay images to the 3DS. If the controller is only streaming imagesand control, it won't need to be powerful tech wise, if ON LIVE is anything to judge by. Since the 3DS had dedicated gaming hardware however -- would it be possible to display project cafe software in 3D on the 3DS?
It would keep the Cafe forward compatible with future home 3D display options.