Just a couple things I thought of that may be rather mundane additions,
but one was Going To Red (internal lights) at sunset and the reverse at sunrise is automatic in SH3; personally I'd like to either do that manually (perhaps a switch close to the Echolot wall), or have an additional box selection from one of the officer icons or something which calls out the command and a crewman carries it out.
Also, there are a few tunes on the gramophone I wouldn't mind either turning down or up when the crew and I are vegging out in cruise mode. What about having the volume adjustable in some way? Someone mentioned a more involved process of receiving messages from the radioman, which would be cool too. Having him respond to a volume up or down on the gramophone shouldn't be too hard.
Too much immersion?