The reason behind the censors in X/Y is Pokemon Amie. When you have Amie open on the bottom screen of the 3DS, there's a chance other people's Pokemon might visit you when you leave a Poke Puff for them.
The names of the players and their Pokemon's nickname are displayed, and given Pokemon games are mostly targeted towards kids there could be a chance the parents might feel offended when they see the name, that's why they block people from naming their trainers or Pokemon any names that contain a blacklisted word.
However, this also affected some actual Pokemon species names in the process.