The fact that you can ONLY buy the CPP at GameStop means there is absolutely the potential for a segmented market. There is probably a fair chunk of 3DS owners (parents, young children) who never go into GameStop - they buy their games at Wal-Mart, Target, Amazon, Toys R Us, and one of the HUNDREDS if not THOUSANDS of other retailers that sell Nintendo products. These customers probably have no idea that the CPP even exists. It's not like Nintendo is advertising the thing.
Nintendo chose to sell the CPP at exactly ONE physical retailer, meaning they had absolutely no intention of this thing ever hitting widespread usage. (See: Sega Nomad) So then why would they suddenly change their mind and put it onto the system, requiring every 3DS owner for the past year to track down a difficult to obtain peripheral (yes, it IS difficult to obtain if only one retailer sells it - you don't think there would be a MAD rush for CPP if the 3DS XL had included a right circle pad?) or face the potential of their 3DS being obsolete?
Nintendo may very well release a CPP XL, but that's the extent of their support of the right circle pad. Nintendo made their bed over a year ago, and now we have to lay in it until the 3DS successor rolls around.