Okay, so for the fist few weeks of ORAS I didn't think Greninja was actually broken. I felt that it was difficult to handle, yes, but manageable. It does have a handful of checks on offense, the playstyle it was notorious for being excellent against. Scarf Landorus-T, Mega Lopunny, Mega-Manectric, priority users such as Bisharp and Talonflame all of these can revenge kill it. These can't switch in reliably, obviously, but offensive teams don't really switch things in as much as loosely check. And Greninja not only gets worn down very, very easily, but also has a hard time coming against anything offensive, so if you're able to force it out a few times you can beat it. Basiclly, if you only consider its matchup against hyper offense I don't find it to be broken.
I started to believe Greninja was broken when I realized that it really wasn't that much of a specialized HO-killer anymore. Well, it is, it's still pretty hard for that playstyle to handle, but not much more than in XY. The most significant thing that changed for it when ORAS came around is that instead of just killing offense, it went on to kill balance too. Oh my lord does this thing destroy balanced teams. It can come in multiple times, and the only common things on this archetype that can switch in and force it out are Tentacruel, Scarf Keldeo, and sometimes Ferrothorn, all of which of which lose to coverage, none of which can switch in repeatedly due to lack of recovery. Basically, the only answers to Greninja that fit on balanced teams now have no recovery, and so get easily worn down. The only actual counters to Greninja that don't lose to coverage (Chansey, P2) are extremely passive and therefore don't really fit on balanced teams.
Even against Stall teams, Greninja puts in work. Against some stalls all you really need to do is weaken Chansey to 65% (really easy; when is Chansey ever at over 80%?) wear down Tentacruel (not too hard, it has no recovery) and there you go you can just rip through it. And if you really want to be mean to Stall you can run Gunk Shot Low Kick Dark Pulse ESens if you want. Greninja puts more pressure on Stall teams than anything this fast or goo against offense should ever be allowed to.
Furthermore, its combination of high speed and coverage means you really don't need to predict much. Literally you can just mindlessly click one move after the next and still do quite well, because Greninja is unlikely to find itself in a situation where it becomes a liability for its team. For instance, you can get Greninja to Low Kick your Lando-T, but Lando-T isn't exactly the hardest thing to switch into generally so that isn't too much of a problem Only situation I can really think of where you need to predict or get screwed over it getting tricked into hitting Bisharp with a resisted move, and even then Bisharp has to win a 50/50 from there with Pursuit. It's not like the opponent can mess around with Greninja much either, so if you've got Greninja in a position where it can get a kill (not hard), it will almost always get that kill. Greninja is a ridiculous momentum-machine all around, it picks up momentum very easily and rarely ever loses it.
As good as Greninja is on paper, it's even better in practice. I think a big reason for that is that some of the most popular Pokemon in the metagame already give it all it needs to cut through weakened teams. For example, Latios puts pressure on Chansey, wears down Ferrothorn, switches into Scarf Keldeo. Lando-T wears down Ferro too, checks Scarf Magneton, checks Lopunny, switches into Sand Rush Drill and opposing Lando-Ts, gives it pivot support and therefore a way to come in for free. And those are both really good, really easily slappable Pokemon you'll be finding on most offensive teams. Greninja has such great synergy with the rest of the metagame that it usually already comes with all the support it requires (which is very minimal support btw) automatically. This makes it very hard to justify not using on any offensive or even balanced team since, chances are, Greninja will already fit on that team fine.
As for 4MSS : This isn't really that true? Or rather, this isn't really a problem for Greninja. It basically has one set right which is basically the best set in terms of overall coverage and consists of Gunk Shot, Low Kick, Ice Beam, and Dark Pulse. This set alone hits the vast majority of the metagame, you do miss out on a handful of things but none of them are too common or hard to counter to the point where not being able to 2HKO them is that detrimental to Greninja's effectivess. It can easily run coverage to get past these extra things, but I don't think this is evidence of 4MSS as much as having the option to hit stuff if your team requires it. Most of the time you'll be sticking to the standard set, the fact that you have the option to hit all those things is just a plus. I really don't think Greninja wouldn't be suspect-worthy if it could only learn Gunk Shot, Low Kick, Ice Beam, and Dark Pulse, it already has enough coverage with these 4 moves alone to hugely threaten most teams.
I think Greninja is broken as a cleaner. Its combination of speed, power, and coverage enables it to run through teams far more easily than any other Pokemon in the metagame, with minimal support or much skill either. It is far too easy to get to a point in the match where Greninja is guaranteed to get a kill without needing to even predict. It is also far too easy to weaken the team to the point where Greninja just wins from there. There is little to no reason to not run Greninja on offense, there isn't a matchup where it will be useless and it can even get past most of its usual checks via coverage. It's too easy to put on teams, too easy to use, too hard to check, and too hard to consistently deal with throughout the corse of a match to be healthy for this metagame.
Ban Greninja