"continue so long? Why were put into storage 'just in case' and, as LO remarked, why were they still seen flying at least two years after the so-called retirement date? Someone hedging their bets?"
There are thousands of aircraft put in storage "just in case"
Retirement from operational service does not inherently mean grounded and never to fly again. If you are really trying to clutch at these straws you are going to have to do better than that. SR-71s were also flown years after retirement. but if it helps the tinfoil hat-- yes they are keeping the fleet of a few aircraft "warm" in case a program that costs hundreds of billions and fields thousands of aircraft, doesn't quiet pan out so you can still go back to the old 40 year plane that has no qualified pilots left for it.
Older aircraft being upgraded means there is not faith in new aircraft? Aircraft being put into storage means expected failure? A few being flown around for research or experimental purposes is suddenly a reflection on the next plane? I don't drink the JSF kool aid but come on. We upgraded phantoms until the end, it didn't mean F-14s and F-15s were bad. And F-4s still fly. The JSFs biggest cheerleaders are upgrading their harriers, this doesn't mean they are cheering any less.
There is something about this aircraft that just brings out the stupid in people on both sides. You have fanboys that think its magic, and detractors that use arguments that could apply to many other aircraft as "proof" that it is poor.