The main reason was as has been stated cost (something like 3 or 5 times times as many maintenance hours per flight hour than the F/A 1

Peter, the reason for the Phoenix has already been stated - to attack large soviet bomber formations before they got within range to launch their AS-4's (a cruise missile about the size of a Mig-15 - designed as a carrier or capital ship killer. In it's day the AWG-9/Phoenix combo was an astonishing achievement, these days even better capabilities are available in the AESA radar in the latest Super Hornets.
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