The Phoenix was never the prime BVR for the US. It was a niche weapon for the USN, to combat the Backfire/Bear threat. Even for the USN, it wasn't the prime; the AIM-7 Sparrow was the primary AAM carried. Tomcats rarely carried Phoenix except when qualifying. It was too heavy, and the F-14 couldn't bring back all 6 to the carrier due to weight. If the Tomcat had stuck around longer, the AMRAAM would have been qual'd for it, and the Tomcat would probably have lost out to it.

And the reason it wasn't used much wasn't just ID issues, but cost. It was supremely expensive, in limited stocks. Why use it against an Su-22 in the Gulf of Sidra? Or waste it over Iraq?