I think here are the reasons why they didn't put the second stick in:
1) Making an XL version of CCP (just listing)
2) Support is being cut off or dim down
3) Consumers might be confused if the design changes too much
4) Developers would've forced the usage into their games, thereby making early buyers feel lefted out buying the early model in the first place and forcing them to buy the CCP(which is a Gamestop exclusive).
5) CCP also includes two shoulders buttons, so they would have to spend more time making the system even more (probably cost more too), also causing more confusion if it had more triggers than the original 3DS. (Goes along with 4 since devs will force that as well.)
This is more or less a future fear. Devs would've force the new inputs in their games and that would've left out the already millions of current 3DS owners. And considering the CCP doesn't become a success or isn't supplied enough, then all future 3DS games might require the CCP to play or it'll feel uncomfortable playing them without the CCP (a la Metal Gear Solid 3D).
This is just a random thought and my own opinion on the matter.
Read my original story on Fictionpress (Shinigami Twin): http://www.fictionpress.com/s/2996503/1/Shinigami-Twin
As well as my other one (Hell's Punishment): http://www.fictionpress.com/s/3085054/1/Hell-s-Punishment
Nintendo Network ID: kingofe3
