Ortiz is not seeing as many pitches to hit. The league has finally realized that he needs to be pitched around. Pedroia is the one that is killing the lineup. If Pedey was hitting Ortiz sees more pitches. Losing Ellsbury hurt both Pedroia and Ortiz. Ells OBP was pretty good and his base stealing ability resulted in Pedroia seeing fastball after fastball, and Pedey is a dead red hitter. I haven't researched it, but I think he is seeing less fastballs this season.
Edit: I am not worried that Pedey's body is breaking down. He is still a great hitter, but this year he has to make a big adjustment this season to the way he is getting pitched. I think he will figure it out. Hopefully, that will happen before it is too late.