They probably did it because of Greninja's popularity, having been voted #1 in a Japanese popularity poll for all Pokemon at the time and having been such a favourite that it got into Smash before it was even in the X/Y games.
In-universe, however, it's lol worthy that Pikachu, Charizard or Infernape don't get any sort of unique bond with Ash, yet a Pokemon that's been with Ash far less time and had far less stand-out battles is somehow the one for him.