It would be really cool if you could select multiple options for a ship. For example, once the galaxy has been explored, it would be nice to be able to park the survey ship in the middle of the galaxy in Guard mode and still have the Auto-survey option selected. This way when a new anomoly is discovered, the survey ship would go right to it without me having to do anything.
Another possible use would be to have a war ship patrolling a sector and have auto-attack selected...
Seems like I am spending most of my time micromanaging ships...especially the survey ship.