I've had a few thoughts about the changes to missiles. Hopefully in 2. 2 Salvo size will not be the be all, end all of missile warfare and adaptability and versatility will become and important part of designing ships and missiles.
In that vein, maybe it would be very interesting to allow for hybrid missile launchers (or maybe just box launchers? Designing a reload system that would accept such a wide variety of sizes would be hellish IRL), that could allow for several different sizes of missiles to be put in a launcher, as long as the total missile size would be below the launcher size.
For the sake of balance this could be done at a size and cost premium, sacrificing firepower for versatility, and allowing us to create truly multirole fighters.
Maybe to avoid any silliness like 20 size 1 missiles in a launcher there could also be a size cutoff under which the missile would not be accepted. Something like 20% of the launcher size maybe?
That would allow us, for example in a size 20 launcher, to put something like 1 size 20, or 5 size 4, or 2 size 5 and a 10, so this seems reasonable.
I think that this would lead to some really interesting designs, as multirole fighters are not particularly viable currently, and mirrors the wide variety of possible loadout current aircrafts can mount.
Regarding chaff, flares and decoys, as you said you will probably allow them to be put on ships. First I think there should be different versions for different types of detection, a thermal seeking missile shouldn't be fooled by a decoy generating a grav sensor return, with the inverse for direct control by MFC or integrated grav sensor. This would allow for some interesting possibilities.
Second, I don't think they should be an infinite resource in a ship, since this would just be a boring flat hit chance decrease. They should have a capacity in my opinion, and I guess a good way to refill them would be with hangars, supply ships and colonies, using MSP to refill them.
Maybe the chaff, flares, etc launchers could be designed component too? With the ability to choose the resolution or signature being imitated as well as the size of the launcher, influencing the chances of fooling fire control and the internal magazine of the launcher. That would allow you to choose between bigger, but fewer launchers that would last longer in battle but have a lower chance to fool enemy hits and smaller, more numerous launchers that would increase their effectiveness but limit the amount available.
Also, since grav decoys will fool grav sensing MFCs, are you planning to make them fool BFCs also?