As noted there were a number of factors affecting USN submarine operations in the Pacific so if you are constantly reading that things got "easier" for Fleet Boat captain's it might be because your sources are flawed, superficial or leave something to be desired.
1. Japanese ASW started off relatively primitive but did improve as the war went on. Their hydrophones and active sonar never achieved the sophistication of the RN or USN but did get better with time. Japanese convoy and escort techniques improved even if they suffered from major institutional and doctrinal flaws rooted in cultural factors like Bushido mythology.
2. The Japanese deployed airborne Magnetic Anomaly Detectors (MAD) before anybody else. There is some debate over whether MAD actually resulted in any kills since Japanese air-dropped ASW weapons often left much to be desired but there is no doubt that submerged boats were attacked without warning having been detected by MAD overflights.
3. Targets became scarcer in the late war forcing commanders to operate take greater risks and conduct inshore operations where ASW assets were strongest and the large Fleet Boat was at a disadvantage. The lack of sizable targets and reduction in kills per day at sea meant was coupled with greater relative losses. There was a similar trend in U-Boat operations but the loss/success curves in the Atlantic were far more extreme.
4. The American submarine service continued to grow but later boats would have suffered from an excess of relatively inexperienced crew members as the talent pool was diluted by continual expansion. Looking at the book The Last Patrol, which details the loss of every US submarine in WW2, the narratives of the sinking often allude to the levels of training, particularly late in the war. The more difficult conditions that came about from the issues identified above (and others) also meant that more late war boats were lost on their first or second patrol.
Defensive weapons and tactics paint only a small part of the picture. The relative increase in sinking's as the war progressed makes perfect sense even if they never reached the catastrophic scale experienced by the U-Boot Waffe.
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