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.