Here are a few my recommendations (with explanations below):
1. Active intercept should be considered a contact.
2. There should be a way to detect helicopters/aircraft other than using periscope.
3. Add refuel/rearm mechanic to helicopters and aircraft
4. Place insertion zones a little bit further from the ports.
5. Remove passive sonobuoy barriers from missions
6. Perhaps add some form of anti-air?