Because the game was designed to fit the default control scheme of the 3DS. The ABXY scheme was already used in prior DS shooters, so they could plan for that from the start, unlike the CCP which came far in development.
It also helps to note that every game so far that got up compatibility with the CPP in a short period of time are games that were designed with a dual analog controller in mind (Ace Combat, Resident Evil, MGS, Monhun, etc.)
In any case, I won't question the technical reasons why Sora couldn't get it in on time, because it's certainly easier to get a game designed with DA in mind to work with the CCP. But there's always the possibility of patching it in later, although it would result in frustration ingame. On higher difficulties, it becomes like trying to play someone with KBM in an FPS using a console controller.