Understood you were referring to the F-22, but the F-35 is not the same aircraft and has a different oxy system.
I'd disagree that it was pure politics whilst totally agreeing that there is a political dimension. However, going on the probation in the first place was a political decision by Gates, who in the same speech suggested a new bomber be developed (although that's all gone quiet).
The project had significant issues on a programme scale that needed sorting out but technical testing for the B turned itself around last year. Lack of Vertical Landing experience was resolved through 2011. I don't think that anyone thought that the initial sea trials would go on time, or be successful, but they did and were. The aux engine inlet door issue quoted by Gates was also fixed by modification, and proven by flight test, which did not significantly alter the weight (don't know about cost) prior to the probation being lifted. What other 'fundamental' issues are you referring to, apart from ones like HMD that affect all variants?
I'm sure more discoveries will come to light, that's what flight test does and the next years will be busy at Pax River. However, the USMC hand is now strengthened by the UK coming back to the B. We upset the Marine Corps by bailing on them once but they seem to have forgiven us and welcomed us back into the STOVL fold, sealed with a loving 72 GR9s.
Netherlands not buying A's would impact, as would Italy changing their buy. But the politicians have to remember that LM have it in writing that pulling out of the buy affects the industrial share of the build allotted to that country. As such any removal of aircraft would cost aerospace industry jobs.