The thing that bothers me about the circle pad pro is that it was treated as an after thought. It's as if Nintendo rushed the 3DS out without thinking clearly enough about how important a second stick/circle pad would be to a handheld that's focusing more on 3D gaming than the DS did. Actually, Miyamoto said that the reason why the 3DS lacks dual analog controls for camera control is because the gyroscope would be effective enough as an alternative solution. The thing is, not everyone is as resourceful as Nintendo is at utilizing control schemes on its own consoles. Some third-parties won't find the gyroscope to be practical enough.
Seemed to me like Capcom wanted it (seeing as how they're the biggest supporter of it), and since Nintendo doesn't have a licensing department they worked on it with Capcom so it could be included in the box with certain copies.
There will not be a 2 stick 3DS and they're never going to require it for any of their games. Ocarina of Time 3D showed that the 3DS's gyro can be used pretty damn well. A port of a game that was made for two stick controllers isn't really convincing me that the 3DS needs two sticks to cater to a minority genre on their handheld.