When US Airways CEO Doug Parker and American Airlines CEO Tom Horton look back at the fruits of their labor in a year from now, they’ll both think that the yearlong courtship and somewhat acrimonious negotiations were the easy part. All they have to do is ask Jeff Smisek, United Airlines’ CEO, who just last month on the airline’s earnings call called 2012 “the toughest year of our merger integration” and said, “We are absolutely not satisfied with the financial results we produced last year.” United merged with Continental in 2010.

The two men and their teams face quite a challenge. The fruits of their labors will determine what passengers will experience before, during, and after a flight...