Pedroia is the better career hitter (not even close in the OPS department), has been the better and most consistent defender (not just per UZR, but most other advanced fielding metrics), more durable (this isn't even a question) and the face of the Red Sox franchise along with Papi.
Not only is he better, he's a lot better, and he means a lot more to the team. He was also willing to negotiate in-season and not try to squeeze every last dollar out of the Sox, unlike Ellsbury and his agent.