Engines, I don't disagree with anything in your posts. Pretty much every modern military aircraft has had issues during 'the early years'.
However, I can't recall another program where "the early years" have gone on for so long. We're looking at a program that was initially launched 27 years ago, with down select to the Lock-Mart design in 2001.
Maybe I'm turning into a cynical old man, but the F-35 program has already lasted longer than some successful military aircraft have gone from cradle to grave, and we're still in the early years?
Back when I was in college, I remember reading a somewhat sarcastic editorial in Aviation Week. It said something along the line of, at the current rate of progression, by the year 2000 the a new military aircraft would be able to go Mach 10, pull 20g's, and defeat any adversary with ease. Oh, and the entire annual USA defense budget would be required to buy one aircraft...