The biggest design problem is a failure of conception:

> The Pentagon sold Congress on the F-35 in part with the idea of creating a common aircraft for three services, alleging it would save money—despite the well-documented and glaring failure of the tri-service F-111 program 25 years before Congress signed off on the very same plan with the F-35 in 2001

The idea that the STOVL variant would have significant parts commonality with the others despite having a giant fan in the middle was pretty laughable right from the start. In general, three aircraft with three very different design mission profiles were not going to be able to share much without making bad compromises.