Unfortunately "Patrol Area XXXX for 24 hours" is the only sort of mission. No picking up spies, infiltrating harbors, etc. (Though on the bright side, a special mission could consist of holding station and reporting on the weather!) There's always hope for SHIV...
SH3Gen is a fun addition. It doesn't change your "mission," but it does make the SH3 world seem a bit more alive, like you're not all alone in the world. I would say the same about the Milkcow mod. Even though neither actually changes your orders, they do add enough to the SH3 world that creativity can take over, allowing you to come up with your own goals. For example, I'll sail patrols with the sole intention of reaching a Milkcow or friendly port (think Das Boot) before continuing on with my "actual" mission.
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