Obviously the power decline has been a big concern with his ISO dipping from .167 in 2011 to .114 this season. His career rate is .152 making this year a big decline. The homers haven't turned into doubles and triples either as he has totaled 40, 42 and 40 doubles and triples combined over the last three years. He could hit a few more in this last few games, but not likely to make a huge difference without a huge finish.
It's possible his power decline is a result of his injuries, but his hit chart doesn't show a huge change in his power hitting. Here is a view of the hit charts:
Even though Pedroia is striking out and walking at similar rates to his 2011 season he appears to be struggling to hit the fastball. According to his Pitch f/x values for every 100 fastballs Pedroia has faced this season he has a -0.08 value or right near league average. That is compared to a career rate of 1.10 runs above average every 100 fastballs.
Looking deeper in the fastball numbers his 2011 season below he faced 1175 fastballs labeled as four seamers. The lower line was his 2013 and he faced a similar amount with some season still to go.
So he faced a few less and there was a higher rate of strikes, but is a 3.2 percent higher strike rate equal a whole drop of 1 run per 100 pitches?
If we take the hit charts and only look at fast balls though:
There is definitely a drop in power according to this chart. In 2011 he has a much larger cluster of hits in front of the left fielder and plenty of outs along the wall. In 2013 he's still hitting a solid amount to the opposite field, but suddenly his pull hitting is gone. Even the infield shows he's fallen a bit behind on the fastball with a larger amount of balls hit to the first base side.
Pedroia clearly struggled with the fastball this season. He wasn't missing the pitch, but was clearly behind on the pitch and this hurt his power. If he was just "behind" on the pitch based on more opposite field contact than maybe it's not thumb related and is something he could figure out and approach better. If so expect Pedroia to slow his decline as he enters his 30's and be even more valuable to the Red Sox under his new contract.