Wolfpacks would be nice.
I would also like to see a better crew system implemented.
I believe that the experience level of each crewmember should be marginally less important than it already is, but that qalification should become massively more important.
It would be fantastic if (for example) very badly damaged systems could only be repaired if an officer with the repair qualification is present in damage control.
I'd love it if officers could gain several levels of qualification: so a "5 star" Medic could bring even near death sailors back to full health in time, but a "2 star" Medic could only prevent their condition from worsening.
Overall I think the skill levels of one's crew should play a far greater part in the success of a patrol than it does now, particularly when things start to go wrong. Ideally, green sailors should even be capable of panic in extreme circumstances!
Losing a highly experienced, qualified and decorated officer should be a massive blow to the running of the ship wheras under the current system I find it has little impact.
Some kind of Nightclub feature ala Aces of the Deep would also be excellent. It could serve as the interface by which you recruit new officers perhaps. Getting drunk and bitching about the fuehrer would be good for a laugh.
It'd also be great if you could gamble with fellow sub captains and bet Renown!
Another thing I'd love to see would be a radio system whereby the broadcasts change depending on the point of the war, and give you updates on what's happening elsewhere in the region. I'm not sure how realistic this would be, but it'd be a thrill.