The problem is not Greninja , but rather Gunk Shot and Low Kick. These two moves give it the ability to check it previous counter in XY. Even though it suffers from 4MSS, it a dangerous game of russian roulette that centralizes the metagame. If you try to adapt to it, it adapts to you. That said, I don't think Greninja should be banned. I believe the best course of action is a complex ban that bans Greninja from having Gunk Shot and/or Low Kick alongside Protean.
Fire Hero, why do you dislike Smogon?
Fire Hero, why do you dislike Smogon?