I've heard that ED is taking over all the missiles, maybe they will fix the phoenix after the R27 / R77 Family rework.
As far as I can tell though, the main issue is the magic INS, the next one being that the mk47A is only rated to 17g irl and the 54C I believe was 25g?
In comparison the AIM-120B maximum allowable G is 30-50g I'd have to look it up again to find the exact figure. Comparatively the 120 should be light-years ahead of the phoenix in maneuverability.
Then their is the issue with the phoenix not supposed to receive pit-bull command on a dropped track . Mean if its fired on a target and track on that target is lost, the missile is dead and will no longer receive guidance or a pit-bull command.
The workaround is if the PH active switch is turned on in the backseat the Phoenix will go pit-bull if the track is dropped, but will not receive guidance. That switch was pretty much never used because you had literally no control over this active phoenix flying around.
But that dropped track logic is more a part of the WCS and not the missile, so I think it'll still be on HB to fix, and since HB hasn't fixed any of the phoenix issues since the F-14 launched, I seriously doubt they will now. Maybe ED will force their hand once they start working on the Phoenix. Or maybe HB is just pushing hard to get the F-14A out before doing more work on the WCS, who knows, they are radio silent on the matter.