Your last point about the Marine requirements is spot on.
They should have designed an Air Force / Navy only version and gotten that fully operational: software bugs worked out, airframe defects fixed, flight/battle tested etc. The costs of the program would be much lower, so more planes, fewer design compromises, more buyers. By that point (which is several years from now) typically there are airframe optimizations and engine upgrades ready that were not available in the initial design. Take those improvements, apply to a dual seat trainer airframe (so you have enough space) and make your STOVL Marine variant. If weight is still a problem consider dropping stealth. Anti SAM and air superiority are a job for the Air Force.
Instead the tail wagged the dog with Marine variant and now we have a big ol' expensive mess.
Re: CAS - I think it is likely to become a drone mission anyhow. Better to have ordinance on a cheap airframe with no pilot. It doesn't matter if it gets shot down and you can have a larger number of cheaper planes. Software flies to and from the battlefield so fewer remote pilots needed - done.