CM - I find it hard to believe that the F-35 program was not designed against a projected threat that would improve during its lifetime. Also, the susceptibility of stealth at the F-117/F-22/F-35 level to VHF radar has been known, even publicly, since the year dot.
The primary countermeasure was to avoid such radars and prevent extended tracking, thus preventing a hand-off to a higher-frequency radar that had the accuracy to manage an intercept. Avoidance was pre-planned on the F-117 (mostly if not exclusively) while the F-22 and F-35 are supposed to be able to locate and evade pop-ups.
We do know that JSF is eight or nine years behind schedule and consequently will face improved threats - more mobile, more powerful and accurate, AESA-based VHF, sensor-fused with AESA tracking radars. All of that makes pop-ups more of a problem, as well as creating the potential recognized by Eurofighter of herding the penetrators into gap zones where they can be more easily detected by fighters.
For the US, the answer may be to improve SEAD/DEAD with Next Generation Jammer, MALD-J, LRASM (which certainly has potential against big emitters on land as well as at sea) and (cough, ahem) certain other assets. It's easier using these assets to get your stealth airplanes through, than to blast a path for radar-shiny jets, so score half a point for stealth. Difficulty: Ivan ain't dumb, hence the Pantsyrs (CIWS for Aegis-on-wheels) to defend the key nodes in the system. (And as KBrockman points out, this is a good early application for DE.)
Which raises the question: if I can't afford all the above enablers (and JSF is doing a very good job of trying to squeeze them out of the US budget), am I on the right track - or would I be better off loading my Typhoons/Gripens/Rafales with standoff weapons + fielding some stealthy UCAVs?