I suspect the variable geometry was no longer needed and made it massively more complex. Meaning more to go wrong and harder to maintain and fix.
That part cannot be upgraded as it is the plane design itself.
Again, I suspect.
You are correct
I remember reading ages ago that the swing wings were incredibly maintenance intensive and the radar cross section was horrendous. There was no way to make them stealthy. On the F35, a single rivet sticking up slightly from the surface degrades the RCS by 1,000 times or more.