How about Depth charges for the PT boats?
Perk point cost definitely a must as well as a limited amount.
Also, they must surfact to shoot torpedoes, unless other sub in sector.
Perhaps limited amount of "underwater" time to simulate battery power instead of diesel so that they HAVE to surface occasionally diesel power and to charge batteries. Not for long, perhaps for 30 seconds, just like weapons reload time.
If sub is near surface, provide VISIBLE shadow under the water and turnscrew wake.
More thoughts to come