I'd like to see some sort of auto-pilot (with a distance limit to prevent ships from bogging down the server). It'd be great to have ships fly to their Way-point while I get up to do something else, particularly when I don't have jump modules. It'd also be a feature that could be tied into the docking system - have a ship fly towards the target rather than teleport.
I think that having auto-pilot circle an enemy while I do a manual override on a turret would also be nice.