The ability to filter out fighter groups/capital ships separately, to reduce clutter.
The ability to organize flights and wings of a mothership from the design window, just like setting up the default magazine settings.
Being able to set fighter wings on default manoeuvres, such as Combat Patrol or Intercept. Being able to modify these orders so you can adjust bearing and distance, weapon's settings and loadout.
Assign default fire control settings from the design window. Maybe make multiple loadouts and settings for different mission types. EX: One setting has multiple small missiles loaded for fleet PD, another has a mix for Ship Hunting.
Being able to designate whether you think a ship type is commercial or not, in the tactical intelligence screen, so you can filter enemy civilian ships out. It should cancel and interrupt if discovered otherwise (like finding out they have weapons).
Make it so larger meson launchers cause more damage. Large meson cannons are practically useless once the focusing tech becomes high enough.
Track company loyalty, lowered by taking over their mining colonies and some such. Allow companies to carry weapons on ships through the use of laws. EX: Anti-pirate law allows one combat ship of 3000 tonnes or less, for every 50000 tonnes of shipping. Ship is allowed railgun, gauss, laser and CIWS.