I think the "fairness" aspect is a little overplayed.
For a .500 team, the difference between playing a perfectly balanced schedule and playing the schedule the Yankees have played (a .514 winning percentage) would result in a difference of 2.5 fewer wins a season based on log5. Those two games could certainly be the difference in making or not making the playoffs, no doubt, but as it is, even 3 more wins and the Yankees would still be mathematically eliminated with one more loss or a win by either Tampa Bay or Cleveland this weekend.
The Yankees have an extreme scheduling disadvantage and even in their case, it statistically didn't make a difference between making and not making the playoffs. I just think an unbalanced schedule in baseball isn't really that big a deal.