On the condition that I could also change the way Japan used whatever equipment I chose, I’d pick the two million tons of additional shipping. Shipping tonnage was one of the most critical aspects of the Japanese war effort, yet it was also an element that they seriously mishandled. The whole point of the war was to secure the resources Japan lacked domestically (such as the oil of the DEI), yet Japan was unbelievably lackadaisical about properly convoying and properly escorting its transport ships to increase the chances that imported materials would actually reach Japan instead of being deep-sixed by American submarines. Britain, in much the same position as Japan and with the benefit of its WWI experience, took the defense of its merchant fleet much more seriously than Japan right from the start of WWII. Japan was also inefficient in its use of transports to keep its troops properly supplied across the vast perimeter of its oceanic wartime front – for instance, transports would sometimes travel empty on one leg of their journey because of poor Army-Navy coordination of shipping needs.
Assuming I couldn’t change how Japan used its equipment, I’d pick the two extra fleet carriers. At Midway, they would have given the Japanese enough reserve capacity to keep two carriers fully dedicated to the job of: a) providing augmented compat air patrol protection to Nagumo’s carrier group; b) scouting for enemy carriers with reconnaissance planes; and c) attacking enemy carriers – if any were found – immediately with a full complement of planes armed with torpedoes and armour-piercing bombs. Some of the reasons the Japanese lost four carriers at Midway were that: a) most of the Japanese CAP was pulled down to sea level when they intercepted the American torpedo bombers, which allowed the American dive bombers to get through; b) the Japanese were desultory in their scouting operations, since they didn’t think any US carriers were anywhere near Midway; and c) Nagumo flip-flopped a couple of time on the arming and re-arming and re-re-arming of his reserve planes (from torpedoes to bombs to torpedoes again), which not only wasted time but ultimately resulted in his being caught with flight decks full of planes and bombs and fuel hoses when the American dive-bombers showed up.