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In Generation 6, a lot of people complained that Greninja was overpowered, so it was banned from OU. (then a lot of obsessive Geninja fans complained about the ban, but that's probably irrelevant) For some reason, the same Greninja now only gets 17% usage in the high OU ladder, and everyone accepts it as just another part of OU. What happened to OU that caused that?

I'm just guessing, maybe gen 7 brought some great counters to Greninja, nerfing its existence in OU. I'm not sure though.
I should point out that even though less consider Greninja to be broken now, it's unarguably amazing and top tier. Greninja hasn't gotten worse at all, there are just enough offensive and defensive checks that it's no longer impossible to prepare for.
Note, usage stats don't always dictate what is overpowered in Smogon's eyes. Plenty of Pokemon have been voted out of OU even though they wouldn't seem much of a problem going by the raw numbers (eg. 6th gen Mega Mawile). I think Greninja will at least be suspect tested eventually, there's a lot that could potentially have it banned. In particular I think Greninja's versitality may get it into some trouble; it's very hard to know if it is using Battle Bond or Protean until you've been screwed over by either one of them. It's not always your fault if you end up in a bad postition due to a Pokemon that you could not reasonably predict, which goes against the nature of a competitive game where you should have an opportunity to counter play if you are good enough at the game. Sure you can scout or sac a Pokemon to find out, but at the same time that is still offering your opponent a lot of control of the game. And it's hardly your fault if you lose because you had to make a 50/50 play to answer either Protean or Battle Bond, and you got unlucky.

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First of all, Bulky Water and Grass types are more viable now then they were. Greninja has a lot of coverage, but it typically leaves out certain moves like Ice Beam, Grass Knot or Hidden Power Electric in order to hit newer threats. The newly viable Tangrowth, Gyarados, Tapu Fini and Toxapex all give Greninja a hard time depending on it's coverage. Gren can run coverage to beat these mons, but then it just loses to other common threats and/or becomes less effective as a general cleaner or revenge killer.

Then you have the bulky steels. Spdef Skarmory, Spdef Jirachi, AV Magearna, Bulky Scizor, Celesteela and Ferro walk all over Gren without specific coverage. The rise of fairy types brought up the rise of poison and steel types, which in turn makes it harder for Gren.

This gen also brought some excellent fast Pokemon and viable scarfers. Tapu Koko and Pheromosa all easy KO Gren. Kyurem-B is an underrated wallbreaker that can survive almost any attack that Gren throws and easily KOs it. It's also fairly weak to priority. It's low bulk means even resisted Sucker Punches and Bullet Punches do hefty damage, forcing Gren out.

Gren actually has quite a lot of checks this gen. Although many of these Pokemon existed last generation, they were less viable and much harder to fit onto teams. Metagame trends (i.e common changes in the Meta) now heavily favour Pokemon that resist Greninja more so than last gen, meaning you can now run bulk grass, water and steel types much easier than before.

Tl;dr stuff that checked Greninja last gen are more viable now and new fast mons and scarfers scare it out. Also 4MSS means Greninja is limited in what it can check itself.

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