I like the ideas!
Maybe a good way to start is to link existing orders to the dialogue screens. For example: "Single sweep", "report nearest contact", "follow nearest merchant" to the hydrophone operator, and "estimated time of arrival" to the navigator. These commands already work in game, and they have appropriate speech assigned to them.
As for the replacement "resource for orders", the most logical to me seems to replace morale by time: using an ability would then take x hours to replenish, and, if possible, experience would be a factor.
Expanding the RPG element will probably involve a lot more work, since you'll need to record additional speech files (or rip them from Das Boot, if that's legal). I think this is low priority for most people, but it would be nice if it could be done eventually. For example: talk to people in the sub pen to get the latest gossip ("No news yet from Kretschmer... he should have come in by now" or "Anyone notice problems with the magnetic fuses lately?"). If dialogues could be tied to the in-game date like the radio news in SH4, there would be enough variety to keep it interesting.
An idea for morale boosting ability: a dialogue option "The Tipperary song if you please" - I'm sure it will be appreciated by all of us
