The project was doomed to this fate from the moment the requirements document was handed down, much like the Space Shuttle's last minute redesign. The F35 is 3 different planes crammed into one airframe.
Some of the aircraft flown by the USAF and the US Navy have higher annual operational costs than the sticker price of those same aircraft. The F-35 is an attempt to avoid repeating the same mistakes, but obviously, easier said than done.
Buy a kayak for $100? You need around $100/yr in storage, cleaning and upkeep for it.
Buy a glider for $10k? You need around $10k/yr in maintenance, hangarage, taxes, insurance etc.
Buy a jet for $1M? You’ll spend that much on a hanger, crew, fuel, taxes, mechanics, parts, insurance etc etc.
Get an aircraft carrier for $1B? You’ll spend that much on crew, ports, maintenance, munition, training etc etc.
Sure you _can_ do it cheaper, but it’s a good rule of thumb from a budgetary point of view.
I think that if nothing else is learned from this program, it's that 'cost estimates' regarding it fit someplace between 'meaningless' and 'fraudulent'.
Designing a plane that can be used by the Air Force and Navy can be done; adding the vertical flight to it, you break it: it makes it fat (aerodynamic), heavy and all this for a use case that is rare and useless to the other branches. For example, an F18 can be used by USAF and Navy, a modified F16 can be adapted to carrier operation with a reasonable cost and still you have good planes. Take one of these and put the VTOL in it: there is no high-performance VTOL plane ever built, so what are we dreaming about?
Then again, I know nothing about designing war planes so.