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Regional carrier SkyWest had the highest involuntary denied-boardings rate last year, 2.32 per 10,000 passengers.

But not every airline overbooks flights in an effort to keep seats full. JetBlue and Virgin America were the industry leaders in avoiding denied boardings, with rates of 0.01 and 0.07, respectively.

United Airlines‘ consumer complaint rate was 4.24 complaints per 100,000 passengers. Southwest had the lowest rate, at 0.25. Southwest was among five airlines that lowered complaint rates last year compared with 2011. The others were American Eagle, Delta, JetBlue and US Airways.

Consumer complaints were significantly higher in the peak summer travel months of June, July and August, when planes are especially crowded.

“As airplanes get fuller, complaints get higher because people just don’t like to be sardines,” Mr. Mann said.

The complaints are regarded as indicators of a larger problem because many passengers may not realize they can file complaints with the Transportation Department, which regulates airlines.

At the same time that complaints were increasing, airlines were doing a better job of getting passengers to their destinations on time.

The industry average for on-time arrival rates was 81.8 percent of flights, compared with 80 percent in 2011. Hawaiian Airlines had the best on-time performance record, 93.4 percent in 2012. ExpressJet and American Airlines had the worst records, with only 76.9 percent of their planes arriving on time last year.

The industry’s on-time performance has improved in recent years, partly because of airlines’ decision to cut back on the number of flights.

“We’ve shown over the 20 years of doing this that whenever the system isn’t taxed as much — fewer flights, fewer people, less bags — it performs better. It’s when it reaches a critical mass that it starts to fracture,” Mr. Headley said.

The industry’s shift to charging for fees for extra bags, or sometimes charging fees for any bags, has significantly reduced the rate of lost or mishandled bags. Passengers are checking fewer bags than before and carrying more bags onto planes when permitted.

The industry’s mishandled bag rate peaked in 2007 at 7.01 mishandled bags per 1,000 passengers. It was 3.07 in 2012, down from 3.35 bags the previous year.

The report’s ratings are based on statistics kept by the department for airlines that carry at least 1 percent of the passengers who flew domestically last year.