[8] A number of design deficiencies were alleged, such as carrying a small internal payload, inferior performance to the aircraft being replaced, particularly the General Dynamics F-16 Fighting Falcon, and the lack of safety in relying on a single engine, and flaws were noted such as vulnerability of the fuel tank to fire and the propensity for transonic roll-off (TRO or "wing drop").

The Joint Strike Fighter program was intended to replace the United States military General Dynamics F-16 Fighting Falcon, Fairchild Republic A-10 Thunderbolt II, McDonnell Douglas F/A-18 Hornet (excluding newer E/F "Super Hornet" variants) and McDonnell Douglas AV-8B Harrier II tactical fighter and attack aircraft, and meet anticipated performance expectation enhancements covering military requirements up to 2035.

Northrop Grumman provides active electronically scanned array (AESA) radar, electro-optical AN/AAQ-37 Distributed Aperture System (DAS), Communications, Navigation, Identification (CNI), center fuselage, weapons bay, and arrestor gear.

[32] In November 2010, the GAO found that "Managing an extensive, still-maturing global network of suppliers adds another layer of complexity to producing aircraft efficiently and on-time" and that "due to the extensive amount of testing still to be completed, the program could be required to make alterations to its production processes, changes to its supplier base, and costly retrofits to produced and fielded aircraft, if problems are discovered".

[41] On 9 November 2009, Ashton Carter, undersecretary of defense for acquisition, technology and logistics, acknowledged that the Pentagon "joint estimate team" (JET) had found possible future cost and schedule overruns in the project and that he would be holding meetings to attempt to avoid these.

Gates insisted the F-35 would become "the backbone of U.S. air combat for the next generation" and informed Congress that he had extended the development period by an additional 13 months and budgeted $3 billion more for the testing program, while slowing down production.

[87] However, the company said that the slowdown in American orders would free up capacity, which could be diverted to meet urgent, short-term needs of foreign partners for replacement fighters.

[96] Testifying before a Canadian parliamentary committee in 2011, Rear Admiral Arne Røksund of Norway estimated that his country's 52 F-35 fighter jets will cost $769 million each over their operational lifetime.

[116] In 2012, Lockheed Martin reportedly feared that the tighter policies of the Obama administration regarding award fees would reduce their profits by $500 million over the coming five years.

[127] In June 2013, Frank Kendall, Pentagon acquisition, technology and logistics chief, declared "major advances" had been made in the F-35 program over the last three years and that he intended to approve production-rate increases in September.

Air Force Lt. Gen. Christopher Bogdan, program executive officer, reported far better communications between government and vendor managers, and that negotiations over Lot 6 and 7 talks were moving fast.

[129] In August it was revealed that the Pentagon was weighing cancellation of the program as one possible response to the budget sequestration[130][131] and the United States Senate Appropriations Subcommittee on Defense voted to cut advance procurement for the fighter.

[136] A 2014 Center for International Policy study cast doubt on the number of indirect jobs created by the program, which has been a key selling point for the F-35 to Congress.

Major General Charles R. Davis, USAF, the F-35 program executive officer, has stated that the "F-35 enjoys a significant Combat Loss Exchange Ratio advantage over the current and future air-to-air threats, to include Sukhois".

[158][159] Consultant to Lockheed Martin Loren B. Thompson has said that the "electronic edge F-35 enjoys over every other tactical aircraft in the world may prove to be more important in future missions than maneuverability".

Osley continued, "these are inconsistent with years of detailed analysis that has been undertaken by Defence, the JSF program office, Lockheed Martin, the U.S. services and the eight other partner nations.

[180] In March 2013, USAF test pilots, flying with pre-operational software that did not utilize the all-aspect infrared AAQ-37 DAS sensor, noted a lack of visibility from the F-35 cockpit during evaluation flights, which would get them consistently shot down in combat.

Defense spending analyst Winslow Wheeler concluded from flight evaluation reports that the F-35A "is flawed beyond redemption";[181] in response, program manager Bogdan suggested that pilots worried about being shot down should fly cargo aircraft instead.

[185] In 2014, David Axe stated design flaws related to its single-engine configuration could vex the F-35 for decades to come, forcing the Pentagon to suspend flying too often for the majority of its fighter fleet.

To address the issue of wing drop and buffet maneuvering, the required control law modifications will reduce the maneuverability of the F-35, "only exacerbating the plane’s performance problems in this area".

"Pilots really like maneuverability, and the fact that the aircraft recovers so well from a departure allows us to say [to the designers of the flight control system laws], ‘you don’t have to clamp down so tight,’" says Nelson.

[194][195] The pilot who flew the mission reported inferior energy maneuverability, a limited pitch rate and flying qualities that were "not intuitive or favorable" in a major part of the air-combat regime gave the F-16 the tactical advantage.

In an interview with CBC Radio broadcast 2 July 2015, military journalist David Axe claimed to have read the leaked report and stated: "Against a determined foe, the F-35 is in very big trouble".

[197] The Pentagon, JPO, and defense analysts have defended the F-35's utility in spite of the report's assertion that it lacks maneuverability by saying it was designed primarily to disrupt the kill chain of advanced air defenses while the F-22 would handle close-in dogfighting, it has advanced sensor and information fusion capabilities to detect and engage enemy aircraft at long ranges before it can be seen and merged with, and that most air combat in recent decades has focused on sensors and weapons that achieved long-range kills rather than close combat.

ALIS supports everything from the plane's operations, pilot scheduling, mission planning and supply chain management to maintenance; it is therefore one of the three major components of the jet, along with the airframe and engine.

GAO said one of the biggest concerns raised by 120 F-35 pilots, maintenance staff, contractors and program officials interviewed for the report was the lack of a redundant system for processing ALIS data.

According to Flightglobal, "F-35 programme director Lt Gen Christopher Bogdan told Congress...that a failure rate of once every 8-10h or greater would be more acceptable, and recent fixes now seem to have achieved that goal".

Their reason is to reduce F-35 life-cycle costs by creating competition within the program and to refine its acquisition strategy and evaluate alternatives that will deliver the best value, long-term F-35 sustainment solution.

[209] In September 2013, Northrop Grumman revealed the development of a company-funded Directional Infrared Counter Measures system in anticipation of a requirement to protect the F-35 from heat-seeking missiles.

[215] In 2016 Robert Weiss, executive vice president of Lockheed Martin Aeronautics, said that buying more F-35s now would make it cheaper to apply planned upgrades to the entire fleet later.