I believe that it does even out through a season because like you said every team gets boned on a call at one time or another. However, I think with the addition of replay less teams would get boned less often.
I don't wanna hear that baseball games are already too long. If you can't stand watching an entire baseball game because it takes too long then you are not a fan of the sport. At least with baseball there is a lot of action in between commercials. Sometimes in football games its 1 play, commercial, 1 play, commercial, 1 play commercial, time out, punt, commercial, kick off commercial. Yes I agree that baseball games do take a long time, but I don't think that in retrospect they take any longer than a football game.