Monster Hunter Tri G was the first game to use the CP Pro and it was announced alongside the game, that was a long time before Kid Icarus. Monster Hunter 4 was also the first 3DS game to use the full system resources. Nintendo had already collaborated with the team on the Classic Controller Pro for the original Tri as detailed in Iwata Asks.
I meant the baking it into the N3DS. The CPP allows for a lot more functionality across the board, its not something that is entirely a peripheral to MH. As I said, they have use for it in their own software and have used it, and it makes sense to bake something like that in as the DS line has been, for the longest time, lacking a secondary directional input for the right hand.