All of the characters in the game were chosen at the start of development. This means Geninja was chosen before Pokemon X & Y was released, and that its inclusion was not because of its popularity.

There was an open slot for a new Pokémon character, and the team began discussing who to put in it, eventually settling on Greninja. All the reference material they had for Greninja were simply drawings at that point. Sakurai went home the same day he received the Greninja reference material and stayed up until midnight to do the motion capture for the character.
Contributed by DidYouKnowGaming