Phoenix missile was there for a reason - to kill Soviet bombers at long distances.
We can think of one or two scenarios where the F-14/Phoenix combo might be of use. Like, enemy deployed one or two airborne radars, each of them escorted by 2-3 pairs of fighters of Su-27 or J-10 class, the fighters located 30-50 miles ahead of the radars. F-14 can lob the Phoenix from 70-90 mile distance on the radars, and safely retreat. The F-18E/AIM-120 combo can't do it, since the enemy has the means to engage the Hornets before those can engage radars. It does not need to be the enemy AWACS platform, they can have the LR MP A/C there.
Or, the inbound strike is discovered at wave top at 300 miles from the surface group, the defending fighters are 100-150 miles away from it and to the side. Again the F-14 can make a dash of 30-50 miles in supersonic speed, and fire the missiles 50-70 miles away with good chance to hit targets at low level. The F-18 cannot do that. Further, enemy fired off it's anti-ship missiles. Phoneix has better chance to intercept, and with bigger warhed to kill the missile. Let's recall that Soviets have had supersonic anti-ship missiles for almost 50 years now, and many of them are exported.
Re-programming the guidance system, or installing the new with microprocessors, can allow for missile to be fired as anti-radiation missile to hit the approaching war ship or a ground-based radar that just started emission, thus no need to carry extra anti-radiation missiles like the HARM. USN can purchase 30-50? Phoenix missiles per each Super Hornet or F-14, plus there is a good deal of missiles in the warehouses that can be refurbished.