When it comes to large fleets of spaceship battles, my favorite vision is from the Honor Harrington series of novels. Missiles are the MOST important weapon in the battles in those books. Battles are usually won by the missile exchanges long before they get into energy weapons range. I don’t know if you’re able to model anything like that in this game, but I sure would like to see it closer to that type of combat. It’s always a game of getting better missile tech vs. missile defense tech.
One issue that still makes missiles ineffective is the tendency for a large group of ships to all pick the same distant target, rather that each picking ships close to them (which would often be different). This wastes a lot of firepower on the hulk of whatever poor ship gets picked and also prevents the missile boats from achieving their best rate of fire, since they often shoot at an unnecessarily long range. It probably also leads to more missiles being shot down by Point Defense while they cross the enemy formation too, but I tend not to notice that much (if I’m going for missiles, I go all out and easily overwhelm any reasonable PD coverage).
Missiles should try to target the closest possible target so they can reload and fire again as soon as possible.