A few things I would like to see, or see improved, in order of preference:
Better game save - save at sea, etc.
Milk Cows and simulation of the reop, refuel/reprovision at sea
Damage model for subs (crushing, etc.)
More under water detail (fish, rocks, coral, etc.)
Better looking sub nets and damage (they look like perforation board)
Ability to move through/explore the sub
More/better shore details (vegetation, buildings, etc.)
Improved map detail on close inspection
Better crew management
Wolf Packs (maybe with communication and control of them, if possible.)