The chief reason was to save money. At the turn of the 21st Century, the Navy saw shifting to the new F/A-18E/F Super Hornet for all seaborne tactical strike operation (and eventually electronic warfare with the new EA-18 Growler aircraft) offered the Navy a fleetwise annual savings north of $1 billion over a multi-airframe tactical aircraft fleet.
There have been several proposals to update the existing F-14 airframes and even purchase a new state of the art variant of the F-14 called the Super Tomcat 21, which Grumman had proposed as the base of a new family of strike fighter aircraft based upon the F-14D. The Super Tomcat 21 would have included a host of new features such as
F110-GE-429 turbofan engines. This 29K pound thrust class engine, a modification of the same variant found in later block F-16s and now some Strike Eagle derivatives, albeit with a longer exhaust pipe tailored to the Tomcat, would give the ST21 supercruise performance (>Mach 1 without the use of gas-guzzling afterburner) while carrying a relevant air-to-air loadout. Some state M1.2-1.4 supercruise would have been possible.
Enlarged and recontoured leading-edge gloves with an additional 2,200lbs of fuel storage each.
Underfuselage-mounted Ford Aerospace (now Lockheed Martin) Night Owl targeting pod/FLIR and navigation pod.
Single-piece windscreen for enhanced visibility.
Wide-angle raster-scan HUD capable of projecting FLIR imagery.
Glass cockpit.
New mission computers and graphics processors.
On-Board Oxygen Generations System (OBOGS)
AN/APG-71 radar with additional upgrades ported over from the AN/APG-70 used on the F-15E. Expanded range and capabilities over the original AN/APG-71 in F-14D, which itself was an outgrowth of the AWG-9.
Digital Flight Control System (DFCS).
Wet wing pylons capable of carrying 300-gallon external tanks.
Ability to carry 425-gallon external tanks on nacelle hardpoints if it was developed. Existing tank size 280 gallons.
Larger multi-segmented fowler-flaps.
Enlarged and extended slats on wing leading-edge.
Bring-back to ship capacity increased from 9k lbs to 16k lbs.
Reduced approach speed and better slow-speed control.
Integration of latest standoff weaponry, as well as AIM-120 AMRAAM.
Upgraded AN/ALE-47 countermeasures dispenser.
Integration of the BOL countermeasures dispensers into the outboard pylons as a mission configuration option.
Such an aircraft would have provided the Navy with the capabilities of, more or less, a navalized F-15E Strike Eagle. But even with all the advanced upgrades that the Super Tomcat 21 would’ve offered, it was still seen as obsolete in the advent of stealth technology, which the Navy really wanted to get available in fighters on its carrier decks.
It is possible that the Navy may have bought Super Tomcat 21s or similar A/C utilizing Low Observable Technologies as a replacement for existing F-14s had the planned successor to the A-6E Intruder, the McDonnell Douglas/General Dynamics A-12 ‘Flying Dorito’ not been such an failure. Facing massive cost and weight overruns and the Navy unable to justify it, the A-12 program was terminated in 1991 by then Defense Secretary Richard Cheney. The proposed NATF, or Navalized Advanced Tactical Fighter variant of the F-22 airplane, then in development in the ATF fly off, was abandoned by 1994 - a victim of post-Cold War defense cuts.
Faced with dwindling defense budgets in the Clinton administration, the Navy was looking for a more conservative and cost-effective option, which it found in a modernized variant of the F/A-18 airplane. This also offered the advantage that the Navy could package and develop the jet under the existing F-18 program, eliminating the need to ask Congress for additional funds for a new and risky fighter program. Finally with Joint Advanced Strike Technology (JAST) program, which eventually morphed into the Joint Strike Fighter / F-35 family, the new modernized F/A-18 airplane offered the navy a more fiscally sound interim solution for fleet defense needs until JSF and other stealth aircraft were operating from their carrier decks.
Today in the face of continued developmental problems with the F-35C, the Navy continues to upgrade the F-18 Super Hornet with the Advanced Super Hornet program.
As for the F 15, it, too, sojourns on simply because the Air Force does not have an available option currently as a replacement. Both the F-22 and F-35 aircraft programs are problematic and costly, greatly reducing the number of aircraft that were purchased. In the case of the F-22, the need for 750 Raptors to counter a Soviet threat which no longer existed. A limited asymmetric war on terror in the 2000s also made the F-22 something of a dinosaur despite being the most sophisticated fighter aircraft on the planet; an airplane with no war left to fight. Perpetual development troubles and setbacks with F-35, reducing annual procurements and limiting fleet size. This leaves the Air Force with no other choice currently but to upgrade it’s existing F-15, F-16, and A-10 fleet of aircraft until a more suitable replacement becomes available. It would be a sad irony indeed, if F-22 squadrons began to be replaced by F-15EX units!
UPDATE: Dear God, my predictions are coming true!
https://www.thedrive.com/the-war-zone/44954/air-force-wants-to-retire-33-f-22s-buy-more-f-15exs-in-new-budget