There are a couple of issues (disappearance on launcher defeat, no retarget on foe defeat) that are core programming issues - those won't get resolved without some serious work involved.
Overkill should be helped somewhat with an increase in missile speed (and I would emphasize having missiles increase in speed as tech improves), but overkill is also happening because the ship targeting equations don't properly account for in-flight missiles to determine if hit-scan weapons or even additional salvos from the same missile launchers need to shoot at the same targets (again). Unless those equations also get updated, we'll still be dealing with (probably quite a bit of) overkill.
The biggest issue I think out there is still PD and Evasion for missiles (and strike craft). Missiles are the only weapon system of the Big 3 that has to deal with a fleet-layering defensive system, and then they still have to defeat the ship-level defenses, for which they have little capability (only torpedoes). (Strike craft actually get it worse because, while they do punch through a lot of the ship-level defenses, if they get shot down even once, they're done for the fight.) Fleet PD cannot continue to be as effective when layered at stopping missiles and strike craft, because it doesn't matter if each missile has 100% accuracy if less than 20% of the missiles get near their targets (versus 100% of the kinetic/energy shots getting through even though only 70-80% will hit).
The layering is the key here: if a single PD counter-attack is only 10% successful at destroying a missile, then a missile attack that should expect to face only 1 PD attack on its way to its target would need to be 111% as effective as a kinetic or energy attack when balanced for accuracy, penetration, range, RoF, etc. But add another PD attack per missile at the same level, and now the missile only gets through 81% of the time and has to be 123.5% as effective if it hits. Or if a Flak Cannon hits less often but always destroys the missile, might be 20% effective per shot, with the balancing needing the missile to be 125% (single shot) or 156% (2 shots). Right now, those per-shot success percentages for PD are a lot higher than that and the layering is pretty extensive, and yet missiles that actually get through are still far behind their kinetic and energy cousins.
Missile speed still has its uses here, too, with higher speeds keeping the number of shots against each missile down. But I'd prefer to see anti-missile PD moved mostly to the individual ship level (more Phalanx gun system and less Aegis missile system) and then have limited low-percentage fleet PD for missiles (to a lesser extent) and strike craft. While the fleet PD would seem to make more realistic sense against missiles, we've gone way past realistic on most everything else on weapons and this would be a poor place to hold some sort of realism line. Individual ship PD will be easier to balance out the effectiveness of missiles versus the other two main types, and fleet PD (including interceptor fighters) would still be there to deal with strike craft, with a smaller chance to defeat larger, less-Evasive missiles.
It's either that or we get podnaughts and Ghost Rider missiles (Honor Harrington novels)...
.png){kind=avatar}
