This is Not a Bug, It is a Feature

Check out the bit starting at 6:00

While the C model F-35 did make successful carrier landings and takeoffs, it required that they had to bypass the Autonomic Logistics Information Systems (ALIS) to operate the aircraft:

The U.S. military ran the F-35 Joint Strike Fighter through a series of tests aboard the USS Nimitz super carrier in San Diego in early November. It performed adequately, with one exception — it needed to send its diagnostic data to Lockheed Martin in Fort Worth, Texas, before taking off. If the most recent exercises are any indication, the F-35 may need to phone home every time it sets out on a mission.

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The possible bad news to emerge from the recent tests is this: The Nimitz didn’t have the plane’s Autonomic Logistics Information Systems, ALIS, on board and so the team had to implement a “workaround.” ALIS is the F-35’s notoriously buggy diagnostic system that can ground fully functional aircraft.

History may one day call ALIS the most frustrating, expensive and counter-productive piece of software engineering that the military has ever created. It’s so bad it’s been on “60 Minutes.” In February 2014, CBS News Pentagon correspondent David Martin showed that ALIS was resistant to human override instructions even when it was forcefully grounding a plane because of a part mislabeled in a database. It was the worst sort of tyrant, both blind and powerful.

The stated goal is more than allowing for more detailed knowledge of what maintenance might be on the schedule, or what is broken.

It is intended to perform prognostics, which would allow parts to be replaced on the basis of actual condition, as opposed to a (necessarily) conservative life span, by looking at the various information on a system and determining when it is near failure, and replacing it then.

The problem is that you cannot fly the aircraft if ALIS says no, which is why they had to make an override, as opposed to ignoring it.

Of course, this would be inconvenient in battle, but I think that there is a method to this madness:  ALIS functions as an off switch, and as such, it allows our military to shut down the aircraft that belong to a former ally turned foe, like Iran.

Additionally, I could see this being used as a threat to forestall independent action, say, for example, preventing Israel from striking Iranian nuclear sites.

Basically, the F-35 is designed to create a Battlestar Galactica Cylon virus shutdown.  (See video)