IMO That is what it really comes down to. Pilot skill ,experience and training. Some pilots even with inferior aircraft were able to fight it out and win against aircraft with superior aspects. Like the Wildcat vs the Zero. Once the pilots had the training and experience that could take on and win against the Zero. Or even the Buffalo. It took on Spitfires,Hurricanes and P-40s and won. Brewster air-to-air victory credits
One correction here: The USN had pilots with as much or more flying time than their Japanese counterparts and often just as much other experiance. Additionally, they had been trained such that their tactics were superior and their gunnery skills far greater (eg., in deflection shooting). In fact, a major reason the F4F and its successor the F6F have a humpbacked appearance is to permit negative deflection shots by raising the pilot's line of sight over the engine. For the British in the BoB what saved their fighter forces is that they had sufficent time in less intense combat in France, over Dunkirk, and then over the Channel before the Luftwaffe came in force to sort out their bad rigid V of 3 formation and attacking in long strings of V's. Had they not had this combat experiance things might have turned out far worse than they did.
Even there, USN pilots (and even most USAAF pilots) quickly knew the strengths and weaknesses of their advisary. Prior to Coral Sea USN pilots already had an inkling that the Zero could not perform high speed dives. Several F4F pilots in that battle used high speed corkscrew dives to shake Zeros. They also quickly discovered the Zero's inability to roll quickly at high speed using this to their advantage too. It is interesting to note that the one of the test pilots of PO1 Koga Tadayoshi's Zero made the following comment in his report: "The general impression of the airplane is exactly as originally created by intelligence - including the performance." The Japanese also failed to make full use of the qualities the Zero did possess. In the early stages of the Pacific War the experianced pilots prefered to make diving hit-and-run passes on their quarry. Many top USN and USMC pilots suggested the best tactics were to scissor with the Zero at high speed until one could manage a head on pass. Another was when a Zero was on their tail to skid the aircraft and chop throttle or take other actions causing the Zero to overshoot. Jim Flatley at Coral Sea observed that the "Nagoyas" (not knowing the correct designation of the Zero yet) had "poor aileron control at high speed." In the end, the demise of the IJNAF was due more to losses of experianced pilots who were replaced with ones with far less ability than due to any inherent flaw the Zero itself had.