I have a question for you today, when you play Super Smash Brothers have you ever considered how characters get picked, I would assume you are thinking they get picked based on character popularity as is the case with Pokémon characters. The recent inclusion of Greninja from Pokémon X and Y in the new Smash Brothers is believed to be because he is popular as a Pokémon. If this is what you think I must be the one to inform you that you would be wrong in your thoughts.
Many of the games characters have never actually been chosen because of popularity. The character roster for the new Smash Brothers or any of the past three entries in the series have actually never been chosen as the game is developed. Prior to the games entering development the rosters have already been chosen so we know that specific characters are actually chosen prior to the release of there actual games. With this in mind we know that Greninja was chosen as a fighter before Pokémon X and Y was even released so popularity never came into play with his choice even though it is what it seems.
I would assume when they were choosing the roster for the new Smash Brothers they probably decided to look at the new Pokémon in X and Y and thought Greninja would be an interesting fighter with an interesting set of skills. Likewise it would be the same case with other characters chosen for the series. This just makes me interested in potential other characters for the new game or even future entries.