Why was Energy Maneuverability theory not applied to the F-14?
The Energy Maneuverability theory is primarily a conceptual design framework. Its role is to be a guideline in creating the requirements for your aircraft.

This is something well above the manufacturer's level of responsibility. The requirements are created by the buyer, like the US DoD; the manufacturer's job is to design a machine to meet them, with some leeway. And not all modern fighters are based on the E-M theory.

It's not impossible to use a new design framework if you were doing a Hornet to Super Hornet kind of 'Hollywood remake'. But otherwise, an aircraft is created to do a job, and that general job persists through upgrades. Every design choice is a compromise; to get more of X, you need to lose some of Y. Only with a major technological leap could you fit more of X without that loss.

The F-14's job was to maintain long-range CAP around the CVBG. It needed to detect incoming Soviet aircraft at the longest possible range and intercept them before they could launch their missiles. 

The USN had very good reasons to dedicate their top fighter to this role. While the Soviet Navy (VMF) has never been a force the USN had to reckon with, the Soviet Naval Aviation (AVMF) has. Its workhorse was the Tu-22, a supersonic bomber with AS-4 missiles; they're large enough to take out a carrier, and, impacting at Mach 3.5-4.5, outside the realistic capabilities of contemporary SAM, AAM and CIWS to intercept. With a standoff range of over 300 nmi, AVMF bombers would be out of the reach of the Californias at the time of launch. This left CAP essential to carrier survival.

For this job, a fighter needs several things. It needs the range and endurance to patrol far enough from the carrier to help. It needs a powerful long-range radar to spot it before launch. It needs good supersonic speed to have a shot at a Mach 1.8 aircraft. It needs to carry heavy long-range missiles to reach the target. 

You'll notice that dogfighting a Mig is not on the list above. It's certainly within the F-14's role, just not as critical as fleet air defense. Attack roles in the 1970s have been mostly filled by Skyhawks, Intruders and Corsairs. The F-14's design, including its swing wing, was a product of its high speed interception requirements, combined with low-speed needs of taking off with limited power and maintaining long patrols.

Even if the E-M theory was fully developed and accepted at the time, it's not likely that following it would have improved the F-14's performance without compromising its primary role. With the end of the Cold War the requirements changed, freeing up the F-14's carrier slots for multiroles with an offensive focus.