The answer is perhaps deceptively simple. The origin of TOPGUN came out of the results of the Ault Report on Operation Rolling Thunder. One of the major findings of the report was that an in depth analysis of air-to-air engagements showed that there were many instances of evidence of pilots showing sub-standard air combat maneuvering skills and especially apparently failing to understand the constraints of their (predominantly missile based) weapons systems (i.e. not being especially cognizant of the "launch acceptability regions" of their missiles), leading to diminished effectiveness in combat.

The formation of TOPGUN addressed those issues head on by educating pilots (in the classroom) about the specifics and applicability of various air combat maneuvers combined with air time in simulated battle scenarios under realistic conditions using aircraft with similar performance characteristics to those they faced in Vietnam to cement those skills through training. As a consequence the air combat maneuvering of Navy pilots went from borderline or even deficient to routinely top notch and pilots who found themselves in dog fights were doing a much better job of maneuvering their planes into the appropriate launch acceptability regions for their weapons systems, leading to a higher percentage of weapon launches with a greater probability of a successful kill. Which, unsurprisingly, led to a higher kill rate.