The new wild card format is about adding some late-season buzz by opening it up to 2 more teams. I have heard some arguments that the new system is supposed to be fairer because it gives more of a reward for winning the division. At first glance that argument may seem to have some merit, but if you look closer it's hogwash.
Under the old system the St. Louis Cards would have missed the playoffs this year with their 88 wins, and Atlanta would have been the wild card team. Atlanta got jobbed in this new setup. Not only did they have to go to a one-game play-in, but a horrible umpiring decision affected the outcome of that one game.
So now the Cards move on to play the Nats, the team with the best record in the league. Was St. Louis at a disadvantage going into this series? Not much in my opinion. For one thing, they were the 'hotter' team, having just won a big game. Maybe their pitching wasn't set up as well as the Nats. But no big deal, as the series would prove. Also, home field advantage for the Nats was no big deal. Home field advantage doesn't mean much in the baseball playoffs anyway. I think visiting teams are at least .500 so far this postseason.
My point is that the new setup has nothing to do with fairness. Bud Selig did it to generate more buzz and more money. He's somewhat of a huckster. Interleague play, All-Star game deciding World Series home field, and now this. He's getting economic results, no doubt about that. But if he tries to sneak any arguments about fairness past us, don't buy it.