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Greninja, from Pokémon X and Pokémon Y, is one of the playable characters in the new Super Smash Bros. During a Q&A session at E3 this evening, Siliconera asked Sakurai at what point the character was chosen to be included in the game.
All of the characters for the new Super Smash Bros. were chosen at the start of development, Sakurai replied, and that includes Pac-Man, who was revealed as a playable fighter earlier today.
Picking up on what we were getting at, Sakurai explained that the development team wasn’t waiting to pull something out of Pokémon X and Pokémon Y—there was an open slot for a Pokémon, and the team began discussing who to put in it. Eventually, after a conversation among the various staff, they settled upon Greninja.
All the reference material they had for Greninja were drawings at that point, Sakurai revealed. Upon obtaining the explanation for Greninja—presumably from Game Freak—Sakurai went home that same day with the reference material and stayed up until midnight to do the motion capture for the character.
So, Sakurai concluded, Greninja’s inclusion had nothing to do with popularity.