While the program costs have gotten out of hand, that is mostly due to lack of discipline by the program management. You cannot blame the primes like LM, P&W, R-R, etc. for agreeing to being paid for modifications proposed by the customer.
Sorry, RR, but I'm going to call for evidence on that statement. As far as I am aware, the actual system capability requirements were established in great detail in 1995-2000 via a few iterations of JIRD (Joint Interim Requirements Document) leading to the JORD (Joint Operational Requirements Document). Boeing and LockMart both proposed SDD programs based on the JORD.
I know of no major changes to the JORD since then, apart from the relaxation of some requirements. The modifications to the aircraft, of which there have been many, were done to meet the JORD specs - in the case of the F-35B in 2003, the design was on track to fail catastrophically.
MSOCS - I'm frightfully sorry if I upset you. But KenV's attempts to inject massive untruth into the public discussion (for whatever reason), and then smugly refuse to back it up, is also offensive, and to characterize it as "professional and courteous debate" is, well, the wet bit in the bottom of a boat.