Ivan this is a fascinating thread, a great deal of fun to read.
You mentioned the Japanese training establishment and its failure to keep up with the US equivalent in pilot graduate quantity and quality. Saburo Sakai mentioned in "Samurai" the IJN set an almost impossibly high standard, pre-war, to gain admission to pilot training for that branch of service. The belief you stated about the A6M being possibly worth the equivalent of 3 comparable Western fighters could no doubt be bolstered by the implied information in Sakai's description of Japanese fighter pilot training pre-WWII. There seemed to be a lot of attention paid by the IJN to instill or improve in their trainess the intangible qualities that go into a superior fighter pilot, what they would call "spiritual strength," and that had nothing to do, strictly speaking, with flying a fighter airplane. No doubt their knowledge their trainees were getting training in kendo, sumo-style wrestling, and other martial-arts techniques, in addition to their flight training, probably increased their idea of the worth of the A6M once they mated it to the supposed superior qualities of its pilots. Taken together this combination came close to being a "world-beater," at least at the beginning of the war. Their training establishment failed to accept a slightly lower quality of graduate, particularly after Midway, in return for increased number of "good" as opposed to "outstanding" pilots. They suffered essentially from the same problem the Germans did - they could never relieve their outstanding fighter leaders to make them competent instructors for the fledglings, as we and the Commonwealth did in that war. They fought until they were dead, hopelessly disabled, or the war ended.
EDIT: Something else in the article, re: the increasingly desperate POL situation for the Japanese air services, rang a bell. The US Navy's submarine service did not begin a concerted effort to sink Japanese tanker traffic until well into the war. Even the belated start of this campaign, which is roughly dated in the article when describing the onset of fuel shortages, caused significant disruption in the Japanese air arms' efforts. What might have happened had COMSUBPAC/COMSUBSOWESPAC made tankers a priority target for US fleet submarines earlier in the war?