I subscribe to the idea that the most important aspect of hitting is not making outs. Pedroia has always had better on-base abilities than Cano. Add to that better D and baserunning, and Pedroia's the better overall ballplayer.
If you're looking at it from a strictly offensive standpoint, even while scaled to their actual values (because slg% is always around 20% higher than OBP) Cano's offensive production is better than Pedroia's overall. wRC+ also subscribes to this notion.
In conclusion, one could argue that Cano's the better hitter because of the difference in power, but Pedroia is the better player, and has less pronounced platoon issues offensively.