As Southwest Airlines goes through the difficult process of folding AirTran Airways' operations into its own, it has taken a tumble in the annual ranking of customer satisfaction, falling from the top spot.

The 2012 American Customer Satisfaction Index, released today, names JetBlue Airways as the new No. 1 carrier with a score of 81. It's the first year the airline has had enough market share to be ranked in the index. Dallas-based Southwest took the No. 2 spot with a score of 77, after 18 years in the lead.

ACSI ranks companies in 47 industries, with today's report covering restaurants, hotels, airlines and consumer shipping.

Airline mergers tend to cause short term passenger dissatisfaction, according to the report.

ACSI managing director David Van Amburg said service providers ranging from banks to retailers to national wireless carriers tend to run into challenges when combining computer systems. In the case of Southwest and AirTran, Southwest has delayed plans for traveler connections between Southwest and AirTran flights. That's partly because AirTran charges baggage fees, while Southwest does not. The merged company wouldn't charge the fees on an itinerary that includes flights on both, so that revenue would be lost.

Southwest spokesman Brad Hawkins said the company is "moving through the process of always improving what we offer our customers."

Even without any computer issues, a merger can still create turmoil for some customers.

"If, for instance, one airline was your favorite airline and it's now being absorbed by another airline whose website is different and their way of doing things is different, that can create some dissatisfaction," Van Amburg said. "Change can be disrupting and dissatisfying."

Delta Air Lines improved its score to 65, in a tie with US Airways. Atlanta-based Delta, since its 2008 acquisition of Northwest, has been "kind of ironing [itself] out," Van Amburg said. Bringing up the rear in the ranking of airlines were American and United.

In other industries, the score for Sandy Springs-based UPS declined to 81, falling from the No. 1 spot in consumer shipping to No. 2. This year FedEx came in first with a score of 82, while UPS tied with the U.S. Postal Service's express delivery with scores of 81.

In the hotel category, Great Britain-based InterContinental, which has its Americas headquarters in Atlanta, improved its score by one point to 77, coming in third.

The ACSI, a national economic indicator, uses data from interviews with about 70,000 customers annually.