A lot of the problems listed by the op and others can easily be fixed via either SH3 Commander and/or simple editing of the relevant .cfg files.

At least one valid complaint, the helmsman still at their stations when on the surface (let alone their hands at the wrong controls) can be fixed with a mod. I don't remember where I got it but I can post it if needed.
It adds more food hanging, water drip, changed interior camera view, and the above helmsmen moving. It does not have all the options FlakMonkey's work does.