The game could really reduce it's micromanaging if a combat prioritizing system were introduced where you could simply order the targets you want a ship to engage, save those lists (with alterable names), and issue these orders to both your own ships, and use them as a mission (eg you pay pirate to go into a system and take out all the illuminators in it)
You can already qeue targets and actiosn for ships, so this shouldn't be a huge programming task (though of course I'm a bit of a code moron, so I might be wrong.)