Sam,There's a good chance the F-35 will carry mostly or only...

Sam,
There's a good chance the F-35 will carry mostly or only sidewinders as does the F-22. These missiles don't emmit radiation as the radar guided AMRAAM does, and stealth is maintained. One needs to consider the entire system rather than only one part ot it. As you say, if (that's a big if) stealth can be countered in th future, then Plan B comes into consideration.
It should be noted that the US retired the Pheonix missle system (along with the F-14) which was the worlds longest range missile. Probably a real good reason for that.