All this talk of 2HKOs, but it assumes the Greninja user is always in an ideal situation - it's forcing out a Pokemon and hitting the would-be counter on the switch.
But when are you really going to get this scenario? Greninja is almost never going to switch into a direct attack. You can bring Gren in after one of your Pokemon faints, but that's hardly ideal. And then there's the case of Greninja trying to fight head-on against any of these things you guys say it handles well. If Greninja can't OHKO, it's going to get smacked upside the head in return.
Take
>>21694696 for instance. This is only applicable if Volcanion switches into the gunk shot. Yeah it's scary to think that Greninja can beat this seemingly solid counter, but what if they're both at 100%? In that situation, Volcanion eats it alive.
AT BEST, you'll get one of those ideal switch-in situations per match, and that's even assuming good team support, like a slow u-turn or volt switch user (Scizor or Magnezone, namely). Greninja isn't as good as you nerds are claiming. All this theory crafting, but little of it will hold up in practice, since Greninja can't take a hit.