Conquest flags to only be bought from regional capitals, at least give the defenders some time to organise a defense for ports that are not right next to major player hubs.
Change winning conditions to - total annihilation or zone capture. For the zone capture, have a small area near the defensive spawn. Have something like 5 minute capture time for 1 ship, 4:30 for 2 ships, 4 mins for 3 ships, 3:30 for 4 ships and 3 mins for 5 ships and maxing it at 5, defense can stop the capture simply by having an equal amount of ships, having 5 ships in the zone prevents capture full stop.
This results in defenders having something to defend, attackers having a clear objective to take control of and it stops run away and hide tactics.