If Major League Baseball wants to speed up the pace of the games, which they've been trying to do for awhile now, they have to do more than just encourage the teams to play quicker. There are some things that can't be changed, which are mentioned by BPEF above me. However, there is one very simple change MLB could make.
Batters attempt to control the pace of the game by stepping out, and pitcher's attempt to control the pace of the game by varying their set times. The Yankees and Red Sox's batters, especially, try to do this. MLB, very easily could make two simple rule changes. For each pitch, once the batter steps in the box, he cannot call time. Additionally, once the pitcher holds his set for a certain amount of time, the umpire will call time. This is the best way, in my opinion, to take any kind of pace advantage away from both teams.
MLB has some problems, and while some are very difficult to correct, others are easier to correct (ex. pace of game and poor umpiring). I can't take their complaints seriously if they are unwilling to take the necessary steps to better the sport.