I would say that in trying to come up with a list, the USN ships have to come last. A submarine just won't see them that much, they are window dressing.
As for the japanese types, yeah, there are a number of classes missing.
Unryo and sisters are basically improved Soryu Class (like Hiryu in game, so Soryu is already there). The US CV in game IS Wasp, so that is there.
I'd honestly think that what would be most needed for the japanese would be small shipping (~1000 tons and under), a Matsu DE, and a Kaibokan.
Such a list really needs to be prioritized based on what will be most likely to be seen by a submarine as a target, or adversary. The small shipping that was turned out in the hundreds and thousands of ships after '43, and the small escorts that were used later in the war would clearly be at the top of the list, IMO.
Many games have limited units vs RL, and the usual solution is for stand-ins to be used, and it works. Many of the IJN DDs, for example, are merely evolutionary changes on earlier designs. So substitutions there are fine, the ships look identical.
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