Aren't most modern threats now in the form of Cruise missiles/anti-ship missiles rather than bombers?
My understanding is the F-14 wasn't even fulfilling the role of long range interceptor the last few years it was in service, which would indicate to me that the role isn't as neccesary as it once was
The AIM-54C had an anti-cruise missile defense role, though I don't honestly know much about it and how capable it was. The APG-71, while probably a better radar than the original AWG-9, couldn't possibly have been as good as the new AESA radars that are showing up on the Super Hornet, no matter how good the missile was (and I don't suspect that the AIM-54 was that great compared to the AIM-120 for that particular role).
The finances of flying a 40 year old, very mechanically complex airframe with basically no commonality with anything else in the DoD and that offered very little in terms of actual advantage in combat is what finally did the F-14 in.
The super hornet does all the relevant things that the F-14 did from an airframe perspective, has a 1-2 generation newer and better radar, and is way more stealthy than the tomcat. Plus it's a LOT cheaper to operate and at least has some commonality with the A/B models.
I have some issues with the way the Navy went about buying the thing - it's basically a whole new airframe and should have been acquired as such - but it's a fantastically capable aircraft for what it is, and was probably the right plane for the Navy. I sort of wish the Air Force would do something similar with the F-16. It's clear that the F-35 and F-22 will never be purchased in the numbers to replace the F-16 and F-15s that currently serve the homeland defense role. Even though the 5th gen fighters are vastly superior to the 4 gen ones in a lot of ways, they still can't physically be located in as many places, and that's a bit of an issue if you're trying to defend the whole country.
A cheaper alternative 4.5+ gen F-16 with conformal fuel tanks, upgraded avionics and such would be much less expensive and almost as capable - clearly capable enough for the HLD role, but that's a whole 'nother discussion.
At any rate, the F-14 was a great plane in it's day. It's day has just come and gone.