>>28930556In the conference where Pac-Man was revealed, a Q&A was held in which someone asked Sakurai how did Greninja end up in the game. He responded by saying that normally Gamefreak tells them what pokemon to add into the game, but this time they were hesitant because the game hadn't released yet, so they brought them dozens of Gen VI designs and told them to add whichever they liked best. After some thinking they settled on Greninja.
I don't remember which page had the actual live transcript of the Q&A, but there are some articles that paraphrase it.
http://www.siliconera.com/2014/06/10/super-smash-bros-characters-decided-upon-early-development/ 