I also want to add to the disscusion. Has anyone ever played games that support the Circle Pad Pro? You would probably say they are better. With Metal Gear Solid 3D, it is much better. But, the thing is it doesn't use the L and R buttons, it uses the ZL and ZR buttons! Resident Evil Revelations uses the ZL and ZR buttons! Even, Kid Icarus Uprising uses the ZR button! You see where I'm going with this? That would mean Nintendo would have to add the new shoulder buttons on the system. No way, can you even play those games with CCP support without using the ZL and ZR buttons. Some bring up they just have to add a second stick, but with games that use the CCP already don't just use the second stick, it also uses the new shoulder buttons. And they can't map any controls either, since like I said, some games use a combination of the four.
So that would mean, they would've been forced to add the new shoulder buttons as well. But, that would've made the system even larger and less portable. Then, people would be complaining about that.
If Nintendo added all of these new things, then they might as well made a new console because of all the new input. 2 new triggers and a second stick. That would've made the 3DS XL look completely different from what it is now and cause confusion to the consumer. Also, devs would be confused too. Why even kept the orignial 3DS if the 3DS XL has all of these new things that the original doesn't have? That would've to balance this by making a slim version, since not everyone wants a larger system. But, then it wouldn't be the 3DS anymore, but the 3DS Pro.
This is too much work and confusion just to add a second stick, and they would've been forced to also add the new shoulder buttons in many cases. You could say they could've forced devs to make two control options for now, but some devs don't even want to use the CCP and some devs use the extra triggers.
This is my take on the matter. I'm sure some will try to work around this one.