I've always felt part of what made the submarine commerce war in the Atlantic and Pacific so different was that Germany and Great Britain had a huge rehearsal called World War One. Between Donitz's working on his wolfpack theories and British research into Asdic, radar, etc, they put a lot of thought and effort into it during the interwar period.
For some reason the knowledge from this bitter struggle never really caught on elsewhere. The US adapted U-Boat technology after WWI, but meandered through a lot of mediocre designs before very fortuitously coming up with the fleet boat in the late 30s, which by it's name was meant to operate with the fleet but turned out to be a fine independent machine. The US also struggled with very unrealistic prewar training and untested torpedo technology.
The Japanese really dropped the ball on their end, however. Being an island nation they really should have paid close attention to the British experience in the Great War. However, having built a navy and a mentality which emphasized the decisive battle and all things offensive it would have taken a major cultural shift for them to have done otherwise.
The US by dint of it's huge industrial capacity and it's alliance with Britain and her superb radar technology was able to overcome it's early mistakes in the misuse of it's submarines. For Japan, it was far too late by 1944 to have switched over to building cheap, dedicated escorts and radar-equipped ASW aircraft. At the time they were most needed their resources were already stretched to the breaking point. Prewar, in lieu of building the white elephant superbattleship
Yamato they probably could have constructed 100
Kaikoban frigates. Hindsight is 20/20.
All that being said the fleet boats were probably the finest submarine for the environment and opponent which they were deployed against. Comparing submarines of different nationalities in WW2 is a bit like comparing apples and oranges. Unlike tanks and planes, submarines don't fight each other. They fight the other side's ASW system.