The inestimable Bill Sweetman notes that many of the problems with the F-35 stem directly from the decision to make the Marine Corps, and their STOVL requirement, a part of the program.
The F-135 engine (43,000 lbs thrust) weights 6,500 pounds. The F-414 (22,000 lbs thrust) weighs 2,445 lbs, so this means that the F135 weighs about 1500 pounds more than the about the same amount of thrust installed for the F414.
The engine is also about $5 million dollars more than two F414s.
Of cours, you couldn’t use 2 F414s for an STOVL aircraft, because the lose of just one engine still results in an aircraft loss, so it’s actually less safe than a single engine variant.
You also had the costs and delays associated with the weight reduction programs, which were driven by the needs of the STOVL B model of the JSF.
I think that it was clear from the start that having commonality with between CTOL and STOVL aircraft would result in additional costs, and reduced performance for the CTOL variants, and that incorporating the capabilities of the CTOL variants would increase the cost and weight of the VTOL variant.
So from an engineering perspective, this is a lose, but for the US Marine Corps, from a political perspective, it was a win.
The Marines knew, even with a (now canceled) British order for for a STOVL aircraft, if they were the sole service procuring this, that it would be much easier to cancel.
The F-35 as a joint Navy-Air Force program was too big to fail, a Marine-only aircraft wouldn’t be, so the Marines made it their program too, which had the (political only) advantage of making the JSF program even bigger and higher to kill.
The JSF is a real microcosm of everything that is wrong with the current US procurement/development process.