In an interview with The Independent, Nintendo president Satoru Iwata explained why the upcoming Nintendo 3DS XL has not squeezed in an extra Circle Pad. According to Iwata, while it would have been "possible", Nintendo would have needed to make the 3DS XL body even bigger in order for the second Circle Pad to fit.
Iwata expands further, clarifying that a second analogue input on the 3DS XL was never a main focus when designing the console, as the size of screen and extended battery life took priority over the extra control stick, although it was something Nintendo looked into:
When we looked at the design of the 3DS XL, we had to look at various factors. One was battery life. One was the overall size of the unit. And we had to make some trade-offs. The choice, if we were going to include the second analog stick, was to reduce the size of the batteries or make the unit much bigger. What we wanted to do was have a bigger screen in comparison with the overall size of the system, so we had various discussions and had to make trade-offs, and this is the outcome.
While there may not be a second Circle Pad on the 3DS XL itself, Nintendo has already confirmed that a 3DS XL Circle Pad Pro will be available later this year.