New tests done, new gameplay fix: I will remove the "Aegis" script that made all capital ships from the Confederation and Kilrathi faction abandon what they do to target enemy missiles. This script will remain on escort ships such as corvettes and frigates, but will no longer be present on larger ones. OTOH, I added a better priority for all other units of these two factions so that they still target missiles, but without going their own way and disobeying orders.
By the way, that test, while it ended early with a connexion issue, had a pretty epic moment when the TCS Victory, having located a Kilrathi light carrier and escorts, remembered Captain Kirk's words and used the third dimension effectively. Eight Longbow, fifteen Hellcat and fifteen Excalibur took off from above the enemy Dubav as it was chasing the Arrow recon flight. The Excalibur flights, under cloak, took position near the Kilrathi carrier group, which had all its fighters from Darket to Vaktoth launched. Meanwhile, the Longbow attack force was closing in, escorted by Hellcat.
The Kilrathi player saw the incoming bombers and sent his fighters to intercept as they were closing torpedo range. The Excalibur chose that moment to attack, as they were behind the Kilrathi fighters. A massive furball ensued, with the Kilrathi distracted at the critical moment and sixteen torpedoes were fired. A quarter of them got shot down by the Kilrathi gunners.
The rest hit home.
That's what I dreamed of being able to do in a game for a decade. This was exactly as glorious as I hoped.