Okay, so this is a bit of a pet peeve of mine
FYI, trying to figure out what set it is does not make it "luck based." Luck would require it to be random, beyond either player's control, and capable of going in either player's direction depending on what was rolled. Just because it's unpredictable doesn't make it any less a contest of skill. Your lack of knowledge of its moveset doesn't make your failure to predict its movements bad luck, it simply makes it unpredictable. It was within your control to have picked a better move. I still stipulate that there isn't any issue when there is actual luck involved in the game, however, unpredictability is an issue
And thus I have a segway
Unpredictability by definition literally means that something can't be predicted, in case that wasn't obvious. Prediction is a very important part of the meta and, alongside team composition and RNGesus, is one of the biggest factors in determining who wins or loses a match. To be truly unpredictable is to be above this factor. Essentially, by being so unpredictable, Greninja automatically moves the game to the player using its advantage. You can never prepare for all possible moves it could be carrying, and thus your opponent has to make a mistake to allow you to properly remove it. Or, it just has to not be carrying whatever move
The thing is, while Greninja doesn't appear to have many weaknesses, like so many other things it still suffers majorly from Four Moveslot Syndrome, Sure it could be carrying Grass Knot, thus allowing it to completely screw over your Rotom-W (oh, actually, just did calcs, NVM that), but what are the chances it actually is? It's practically required to have Hydro Pump/Surf, and not having Ice Beam takes out a lot of your coverage, so that's two moves that are essentially guaranteed. Sure you can not run one of those, thus giving you an advantage of unpredictability, but to do so you sacrifice a lot. The movesets that do the most damage are the most predictable, and the ones that are the least predictable, will do the least damage once they're revealed. There's no reason you shouldn't predict it's going to Ice Beam your Landorus and go ahead and switch to that Rotom-W. To not do so is overthinking the situation, and if you're overhtinking by that much, you're going to lose anyway
To emphasize the moveslot syndrome, Alakazam can run moves that let it kill most of it's counters, but it's still laying down in UU. It doesn't have quite as good defenses as Greninja IIRC, but it's still worth noting that you can calc just about anything to make something look invincible, but it will still be limited. However, there is one major factor that puts Greninja above all others in unpredictability
(This next bit is a bit ranty and repetitive, there's a TL;DR down below if you need it)
The main issue Greninja has in unpredictability, and the thing that makes me think it is truly unpredictable, and thus above 1/3rd of the meta. It can run physical and mixed sets, and it can run them well. While the special set in and of itself will always be limited and you can generally assume it has such and such moves, until you've seen the team around it, you can't guess whether Greninja will be physical or special, let alone which moves it has. Of course if you're actually good you can do that once you've seen the team, thus removing the unpredictability, but I digress.
Greninja has several factors that make it completely above predictability. Unless one is skilled enough to solve its moveset based on the team it's built around, it's going to get at least one kill, probably more. But therein lies the question, if this is really about skill, and a skilled player can predict the "unpredictable" Greninja, why should that be a factor to whether or not its considered overpowered? Banning something just because you personally can't figure out how to beat it isn't competitive at all. I still can't figure out how to beat Talonflame half the time, and that's not even that good (At least compared to Greninja)
That's long winded and probably doesn't make any sense with all my apparent back and forth on where I stand, so here's a TL;DR for all that:
Greninja is insanely versatile, and completely unpredictable to many. It requires legitimate skill to best. But it's also relatively easy to best for those who possess enough skill.
To finish, one more question: Where do we draw the line? When is there too much skill necessary to beat something? We talk a lot of how we want this game to be skill based, but if we remove things we consider to hard to beat just because we aren't skilled enough to do so, even though with enough skill it is technically possible. Are we being competitive, or just wanting to win more? Because believe it or not, those are far from the same thing. But then back again, when is there too much skill required? (Whoops, that was more than one ) I remain uncertain of where Greninja belongs, and thus, these are my reasons as to why it should be suspected