Two Suggestions, though I haven't torn through this thread in a while, so I'm not sure if these have been covered. . .
First, Parasite Naming theme based on assigned group:
The idea here is that a naming theme can be a assigned to a sub-group, and, possibly, only to parasites within that subgroup. When a parasite is transferred to that subgroup, it is automatically renamed according to the naming theme. Making it easier to apply callsigns to Parasites. The purpose is purely for flavor, where your fleet has callsigns for different fighter groups.
Second, Covert/Submarine Patrol Order:
An Advanced order for reconnaissance craft with low signatures/stealth capability. This order will automatically assign headings and speeds, based on fuel status, its signature, its own sensor range, and known enemy sensor ranges, to scout a system for contacts. The idea here is that a ship will automatically scout a system, but avoid detection. As well, for "long duration missions" it will keep its speed low during patrol to conserve fuel, but increase speed as necessary to avoid detection or evade hostile ships. An additional thought, an area within the system could be designated for the patrol order, or boundaries set, to limit the search area.