After an $8bn makeover, New York’s new LaGuardia airport complex is finally an airport the city can be proud of. Unfortunately the same can not be said for the industry it serves.

For the second time in almost two weeks thousands of flights were canceled across the US on Wednesday – this time because of what appears to be a snafu with an antiquated computer system. Passengers have had enough.

“It’s been rough this last couple of years,” said Deb Alexis, who had traveled to New York from Orlando. “The flight was great but now there’s stress because the bags haven’t come. Seems like there’s a lot of confusion and delays nowadays.”

Asked if airline travel is becoming altogether too much trouble, Danny Dividu, on his way to Georgia when his Southwest plane was canceled, said simply: “Hell yes. Now I’ve got to go back upstairs to check in again. I usually go Greyhound. Best way to go. I hate flying. It’s too much hassle, always has been.”

Another day, another crisis at US airports.

It might have been the cascading weather-related disruptions the US experienced over the holidays, or computer issues, scheduling, pilot or crew shortages but the outcome was familiar: customers left in a helpless state of air travel limbo.

Whatever the precise cause of Wednesday’s issues, they are part of a wider set of problems for travelers, airlines and the FAA, said Robert Mann, a former airline executive who now runs the consulting firm RW Mann & Company.

“The FAA runs on hardware and software that is in many cases decades old,” he said. “And it’s a multi-year effort to build and install them.”

Even a small, regional failure can have knock-on effects for the entire network, he said, but this “seems to be a system failure” and travelers could expect more issues unless something is done.

The FAA estimates that delayed and canceled flights cost the US economy $33bn in 2019. “Everyone – the department of transportation, the general accounting office, Congress – agree that there is a significant cost to this but nobody does anything about it,” Mann said.

Congress is set to debate the funding of the FAA this year and the hearings are expected to be heated. The FAA is currently without a leader and has been since last March.

Biden has nominated Phillip Washington, currently the chief executive of Denver International Airport, to the position. But his nomination has been clouded by criticism of his lack of experience in the aviation industry and ties to a corruption scandal.

With Republicans now in charge of the House, Biden’s nomination looks more uncertain and the latest mess will expose the transport secretary, Pete Buttigieg, to more criticism following the chaos at US airports over the holidays.

After the flight restrictions were lifted, Buttigieg said his department was not ruling out the possibility that nefarious activity was to blame for the computer system outage.

“We’re not prepared to rule that out,” Buttigieg said in an interview on MSNBC. “There is no direct indication of any kind of external or nefarious activity, but we are not yet prepared to rule that out,” Buttigieg said.

After the incident senator Ted Cruz, the top Republican on the Senate committee on commerce, science and transportation, called for congressional reforms to the FAA.

“The flying public deserves safety in the sky,” the Texas senator said in a statement. “The administration needs to explain to Congress what happened, and Congress should enact reforms in this year’s FAA reauthorization legislation.”

Wednesday’s incident, Cruz added, “highlights why the public needs a competent, proven leader with substantive aviation experience leading the FAA”.

By mid-morning, the FAA issued its fifth bulletin. “Normal air traffic operations are resuming gradually across the United States following an overnight outage,” the agency said in a statement.

By then, it was too late for many passengers. Jordan Cousins, 25, on his way to Nashville on Southwest from New York’s LaGuardia, said his Southwest flight had been delayed twice and then canceled entirely.

“It’s this and then it’s that. You never know. You may have a smooth flight or there may be a problem. It may be at the counter, with the plane, or something,” he said. “Plans never go as planned.”