Included for the first time in the official Airline Quality Rating, Virgin America ranked first in overall performance, though industry-wide complaints jumped by 20%.

The US airline industry’s annual report card, the Airline Quality Rating (AQR), revealed on Monday that 2012 was a good year for US airlines and flyers. In fact, it was the second-best on record since researchers began tracking carriers’ performance 23 years ago – bested only slightly by 2011. Despite this, passengers were more active than ever in voicing their complaints.

AQR researchers evaluated the 14 major US airlines, from American to Frontier, on four main performance evaluators: on-time arrivals, baggage handling, bumping of passengers and customer complaints.

Compared to 2011, more passengers made it to their destinations on time with their bags. On-time arrivals improved by 1.8% and baggage handling by 8%. However, nearly 25% more flyers were bumped from flights in 2012 and customer complaints jumped 20% -- both whopping increases.

United Airlines had the highest complaint rate, almost double the prior year, while Southwest had the lowest. According to the study’s authors, mergers tend to negatively affect an airline’s AQR – United is still smoothing out its merger, finalised in September 2010, with Continental, which could explain its lofty complaint rate. United, the largest airline in the world, also ranked last in overall performance – the same placement given by the Wall Street Journal in January 2013 – though it moves a much higher volume of passengers than most of the other evaluated airlines. United, for example, had 527,000 domestic flight departures in 2012, while JetBlue had 227,000.

“Nearly a third of the customer complaints for 2012 were for flight problems, such as unplanned schedule changes, delays and cancellations,” said Dean Headley, co-author of the report.  Complaints, unsurprisingly, were highest during the peak summer travel months of June, July and August when the planes and skies are the most crowded, affecting flight schedules and overbooking.

Virgin America, which began flying in US skies in 2007, was included for the first time in this year’s report and emerged as the all round top-performing airline. The airline also ranked first in baggage handling and had the second-lowest rate in bumping passengers due to overbooking. JetBlue, number two overall, bumped the fewest passengers out of all the airlines.

AirTran, which earned the top spot in last year’s report, fell to number three this year as it continues its merger with Southwest Airlines, which ranked seventh.