Lockheed-Martin promised that the F-35 would have support costs near that of the far smaller F-16, because of it’s advanced logistics software.

Right now, it looks like it will cost more to operate than the twin engine F-15:

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This specific problem was resolved quickly, but that is not often the case. Across the F-35 enterprise, operators are struggling with severe maintenance challenges of which the most critical are a spare parts shortage, insufficient repair capacity and excessive glitches in the ALIS logistics system that tracks the health of the fleet. Meanwhile at the production level, suppliers and skilled workers are making mistakes that slow down the manufacturing process before a complete aircraft even comes off the line.

The sustainment challenges are emerging at a pivotal time for the program, with F-35 pilot training ramping up, international deliveries accelerating, and the Navy on track to achieve initial operational capability of its F-35Cs in 2019. As the global F-35 fleet is poised to triple by 2021, government and industry officials are facing mounting pressure to solve these challenges—and fast.

Reports emerged recently that the U.S. Air Force—the F-35’s single largest customer—would be forced to cut as many as 590 F-35s from the overall buy, or one-third of the force, if sustainment costs do not come down. The government-industry team must find a way to reduce operations and sustainment (O&S) costs or F-35 customers will have to make “tough decisions,” Air Force Secretary Heather Wilson said ominously during a recent event in Washington.

The Air Force is working with the JPO to reduce overall O&S costs by 38% over the next 10 years, or about $3.8 billion a year, Wilson says. And in the field, the Air Force aims to get the cost to sustain the F-35 down to that of sustaining a legacy F-16, according to Chief of Staff Gen. David Goldfein.

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The main F-35A training hubs, Luke and Eglin AFB, Florida, arguably are facing the most immediate challenge as the Air Force grapples with a critical pilot shortfall.

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But it is not just the training bases that are impacted by the spare parts problem. Overall from January through Aug. 7, 2017, F-35s were unable to fly because they were awaiting parts on average about 22% of the time—more than double the Pentagon’s goal of 10%, according to the Government Accountability Office (GAO).

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ALIS, the maintenance hub of the F-35 enterprise, was designed to ease the burden on maintainers by increasing automation. But today the system, which is based on a 1995 architecture, actually is adding to their workload.

ALIS has an excessive rate of “false positives,” where the system mistakenly tells the maintainers a certain part is broken. Even more troubling, each service continues to rely heavily on contractor-provided information technology experts, rather than service personnel, to manipulate ALIS’s intricate software and complex databases, according to the subcommittee chairman, U.S. Rep. Mike Turner (R-Ohio).

In the field, maintainers must rely on inefficient workarounds and manual tracking processes when ALIS is not performing as it should, officials say. In some of the Air Force’s maintenance units, for example, airmen are assigned to tackle ALIS glitches as their primary job, says Harris, which was certainly not in the original plan.

(emphasis mine)

Lockheed-Martin developed a tightly integrated system as a way of maximizing their ability to lock in customers to their support services,

So you have a gargantuan mass of interdependent code, and fixing problems is like untying the Gordian knot.

The F-35 is never going to be as cheap to operate as an F-16, the JSF’s MTOW is 65% more than the that of the F-16, but right now, it’s simply too expensive to operate in significant numbers.