Shafting Greninja will never make sense to me; it's the most popular pokemon in the world and sells tons of merch and generated insane hype for the anime. Regardless of how you feel about its design or Ash Greninja, it got into Smash before Ash Greninja was revealed, its return in the anime was highly anticipated (and squandered like the whole Masters 8), and it was a competitive powerhouse in gen 6 and 7. Gamefreak has a new pokemon they can shill that wasn't forced into popularity, and they not only immediately drop it but go back and remove tons of what makes it good (protean nerf, battle bond, being in the game at all).