For almost two decades, Southwest airlines has sat comfortably atop the American Customer Satisfaction Index’s annual survey of air carriers. But not only did Southwest’s numbers slip a bit in the new list, it also ceded the lead to JetBlue.

This is actually JetBlue’s first year listed among the major U.S. carriers in the ACSI survey, and it came straight out of the box with a score of 81, four points higher than Southwest, and tying that airline’s record-high scores from 2009 and 2011.

Speaking of Southwest, its drop from that impressive score to a still impressive 77 was blamed, in part, on the airline’s merger with AirTran.

“Airline mergers tend to create significant passenger dissatisfaction in the short term as operations are combined and consolidated,” says Claes Fornell, ACSI founder. “Southwest’s share value has declined 20% over the past year while the rest of the market stayed largely unscathed, with most major airlines flat or improving.”

But a tough merger is not the end of the world for an airline. Following its acquisition of Northwest, Delta had disastrous score of 56 in last year’s survey.

But 2012 was a comeback year for Delta, where the score jumped more than 16% to a score of 65, leap-frogging the airline over United and American with scores of 62 and 64, respectively.

Once again, the aggregate number for smaller airlines beat out almost all of the majors with a score of 74, while the entire industry averaged a score of 67. Of the majors listed in the survey, only Southwest and JetBlue scored higher than the independents or the industry as a whole.

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