Some suggestions for cutting down on micromanagement in large games:
Alien Ship List - Like the F6 "Ship List" in SE4, only it displays all visible ships belonging to other empires. This would allow you to find the one ship that your fleet is pursuing, or just keep tabs on enemy forces in general. Of course, you'd only be able to get full details on a ship if it's within LRS range and has no jammers
Ship List "Summary By Location" Toggle - For the ship list and alien ship list there would be 3 options: Full Display, Summary by Sector, and Summary by System. Full Display would be like the current ship list. Summary by sector would condense all ships belonging to an empire in a sector into one entry, simply saying "83 Alkapi ships in Zetabed sector (3,5) (orbiting Zetabed III)" or something like that. Summary by system would condense the whole system to something like "158 Bulratho ships in Gordassia system". That way you wouldn't have to click on every triangle system or run intel to find the ones with lots and lots of ships!