In brief, there were a set of three interrelated factors that were at work in the Pacific War that worked against Japan's effort during the war.

1. Training Establishments: Obviously, a plane needs a pilot and although the Japanese government instituted programs to cultivate air-mindedness among its population in the 1930s, the Japanese training establishments for both the IJA and IJN were highly elitist and geared to producing only a small number of pilots. The IJN in particular was notoriously selective for its pilot training process and memoirs by surviving IJN aviators like Saburo Sakai describe aspects of training that verged upon hazing to weed out weaker candidates. The result was that in the 1930s, the Japanese had a corps of very highly trained pilots, but one whose numbers could not be replaced easily. Starting in 1940/41, the Japanese tried to streamline the training process, but the older training habits and structures were much harder to break. The fact that the Japanese frontline units were reliant upon the trained cadre of prewar aviators to function meant that experienced flight leaders were less likely to be cycled back into the expanded training units. Japanese training policy stood in stark contrast to the American one, which in the late 1930s made a clear commitment to expanding both its training facilities and pilot programs. The US focus was less upon creating an small elite cadre of fliers, but instead a large number of good fliers. While these pilots did not have the equivalent flight hours as their Japanese counterparts, there entered into combat with enough flight experience to remain competitive. The US training program was thus much more easily able to replenish losses in the air battles of 1942 and 1943 than the Japanese.

2. Resources: The ability of the US to commit to such a large training program reflects the vast amount of natural and industrial resources at its disposal. This ensured that not only could the US commit to supplying the training establishments with up to date equipment, but the quantity and quality of its frontline aircraft increased as the war progressed. In contrast, Japan faced shortages of aviation-related material across the board from 1942 onwards. Fuel in particular was in short supply and Japanese pilots increasingly had less flight time in training due to restrictions in fuel allotments. But the Japanese deficit in resources was not just in raw materials, Japan lacked the equivalent human capital of the United States. Although Japan had industrialized in the late nineteenth century, industrial culture had yet to reach the whole of Japanese population. Many Japanese military recruits lacked working experience with technical machinery and the Japanese training establishments had to incorporate basic mechanic training into their syllabi. Even though their American counterparts had experienced the Depression, far more of them had experience with machinery like cars and tractors than their Japanese opposites. Where this disparity was really apparent was in the the training of aviation mechanics, fitters, and other support personnel. Aircraft are highly sophisticated technical equipment reliant upon regular maintenance for peak performance. Japan could not make good the losses in these support personnel in the battles of 1942 and 1943. For example, although the Japanese losses in pilots was actually not that severe during the Battle of Midway, the loss in trained mechanics and other service personnel was quite severe. Similarly, the Allied tactic of cutting off Japanese island bases and letting them wither on the vine ensured that a corpus of trained personnel was left on bases like Rabaul when their pilots evacuated via either air or submarine.

3. Compounding Factors: The above two factors often worked in tandem to the detriment of the Japanese. A replacement American pilot in 1943/44 frequently had greater flight hours, flew a more advanced aircraft that was better maintained, and in formations that outnumbered their Japanese enemies. The result was that the good American pilot flew in a combat situation that was highly advantageous to him. This allowed already good pilots to hone their skills in direct combat where they became even better. This led to one Japanese commander to liken aerial counterattacks to the American offensives to throwing eggs against a wall. Because mass conventional aerial attacks were paying less dividends, the Japanese increasingly relied upon unconventional tactics to even the odds. In addition to suicide tactics, the Japanese also trained special forces to attack in adverse weather or husband the remaining aces into elite units like the IJN's 343 Kokutai. These units exacerbated the existing problems the Japanese aerial establishment faced as the war drew to its conclusion. Elite units never really accomplished much in the face of American numbers, special attacks, whether suicide or adverse weather, ate up reserves of aircraft, fuel, and pilots.

In hindsight, there is very little Japan could have done to escape the outcome of the aerial war. While it is certainly true that Japan could have taken measures like expanding their training establishment sooner or reducing the vast number of aircraft models parceled out between the IJA and IJN, this would not have erased the material disparities vis-a-vis the US. Given this vast discrepancy, the ultimate ally of the Americans was time.

Because the US and the Japanese/Germans had different systems for their pilots. German/Japanese pilots tended to keep their pilots on the frontlines until they died whereas Americans rotated their pilots back home to train new pilots or test new airplanes after they complete their tour of duty.

This meant that the Japanese/Germans had some very good aces on the frontline, the Luftwaffe in particular had aces who literally shot down hundreds of enemy airplanes, but the Americans benefited form having their aces train pilots back home. Once the Axis aces get shot down they are gone but new American pilots would benefit from the experience of combat aces through their training.

Also USA had Air-Sea Rescue (ASR) programs which were intended specifically to save lifes of pilots who were 'landed' in Pacific Ocean.

The Navy set up submarines stationed at intervals between the Marianas and Japan that acted as lifeguards for downed crewmen.

Source: Stephen Tucker, World War II at Sea: An Encyclopedia.

AFAIK Japanese didn't had anything similar and that contributed to their significant pilot losses.

Edit: there's a PDF on Air Force Historical Support site as well: http://www.afhso.af.mil/shared/media/document/AFD-100929-010.pdf - 'Search and Rescue in Southeast Asia' by Earl H. Tilford Jr.