Couple of thoughts on a couple of different subjects in this entire thread:
1. Missile Agility NEVER made sense, that's not how missiles work in real world physics. AAM's and SAM's in atmo both are either direct fired "tracking" objects which have advantage of no G limits and smaller mass, but don't have any actual avoidance agility. Physics makes making any drastic change to a course once massive acceleration has occurred in a vector very hard to overcome the inertia.
2. AMM's should be "Flak" burst weapons to begin with, they shouldn't have to "hit" another missile directly, just get within 10k of it, detonate, and the shrapnel does the rest of the work. This would make AMM's more effective baseline since a wave of AMM's versus a wave of ASM's would result in the percentage to kill any given ASM to be given to each AMM independently, in other words, salvos target salvos but the calculations to hit are done on a per AMM warhead. So 10 AMM's versus 10 ASM's would get a total of 100 "to hit rolls". This further makes AMM's a great AMM tool, and a poor ASM tool.
3. To counter this, along with PD, ECM values on Missiles would work on a margin efficiency increase while ECCM would be a a direct reduction of that increase. So a 50% margin increase would mean the salvo size would appear to be TWICE as large, in other word every AMM or PD "hit" would have a 50% chance of hitting a "ghost". To make this "fair" and applicable to ships, the simple solution is to use the same mechanic used for engine boost, and missile ECM is twice as effective as ship ECM, but all ECCM is the same "level". This makes the trade for warhead strength and ECM a "fair" one. (This is basically making DECOY ECM or SENSOR GHOSTS which makes targeting the correct target harder, for AMM's it is assumed they will "spread out" to hit the entire ASM salvo. This is a feature which can be ADDITIVE to the sensor/FC/missile JAMMING ECM, perhaps it should be a new technology of DECOY which is basically the opposite of STEALTH)
4. Laser Warheads should be some combination of lasers and particle beams. Hard max range of 120 km, with the range efficiency being the throughput efficiency, so start with 10k end with 120k and fractional damage would still apply. So a Laser Warhead damage would be WH size*Laser Warhead Strength/(Distance/Laser Warhead Range) meaning the base 10k Laser Warhead range with a total Warhead Strength of 10 would do 0.833 damage at 120k km and the full 10 damage at 10k km or closer. This is more aligned with "hard sci fi" use of laser pumped bombs on missiles, then having a "shotgun" approach to try hitting everywhere a target might be in the next 5 seconds.
5. There should be no way of knowing what type of warhead a missile has equipped until they actually go off. The danger of "recognizing" the difference is that it makes gaming the system MORE possible. Just given the above suggestions are taken, if I know that laser warheads are going to be prioritized over nukes, then why wouldn't I put a single laser warhead in a salvo, let it take ALL the prioritized PD and before the next cycle goes off, the nukes have already exploded. Just treat salvos as salvos and don't give any unrealistic "gamey" information to guide the AI decisions.
6. Add BFC to the options to be put on the actual missile, have it work just like the Active Sensor does now, with a realistic Laser Warhead range of sub 1 light second range, it won't need to be grandoise, and doesn't make there be confusion of needing BFC's to control a function of a missile on the launcher itself. Which also means that Laser Warhead mines will be possible.
7. Retargeting missed ASM's with AMM's is simply not physically possible. Now if the pitch is to continue on and potentially target another salvo, maybe, but at a "slow" speed of 20km/s it would take two "tics" for the AMM's to get back to the location where they initially MISSED the ASM's, and then still have to be able to catch them. And that is given a very unrealistic scenario of instant turnover and taking advantage of the flat speeds versus actual acceleration which should be used while under power.
8. Retargetting of ASM's on ships could be doable, but then again, have to run the PD gauntlet twice. It is an interesting idea, which in reality would never come up, because missiles would go "ballistic" well before they ever hit their targets, and in space the amount of inertia that is built up during the acceleration phase would be too great to have enough fuel remaining to be able to do a turnover and re-engage.
9. Missile armor makes no sense, penetrating warheads do but really they are KKV's then in regards to hitting a spaceship.
10. MFC should have a tradeoff between size, range, and number of missiles controlled. Having one MFC for every 10 missiles seems like a good baseline, range to active sensor range for those 10 and then have it go down linearly so double ASR is one missile. Tech upgrades to reduce size, reduce falloff effect, and/or increase base number of missiles.