At the moment I am leaning toward some type of very short range (10,000 km max), very long recharge (at least several hours) weapon or EW system that would attack all missiles about to hit that ship. It would cause perhaps 1 point of damage so it wouldn't be that useful in an anti-ship role and it would be wasted against small salvos. It wouldn't eliminate the massed salvo but it would give the attacker player something else to consider. The idea for this came from the static screens (I think that was the name) in Traveller. This won't be in v4.0 because i need to give it some serious though. I will probably include this when I do the EW overhaul.
Steve
I think that idea has a lot of merit. Sort of like an SFB wild weasel or T-Bomb or such. Be very careful though that it doesn't become too cheap to deploy in quantity and thereby unbalancing. Note that SFB WW's and TB's are both artificially limited in SFB to avoid such problems. The balance point is going to be fairly small IMO.
Here is another idea along the same lines: Instead of destroying all missiles in flight how about a system that for lack of a better term "stuns" a percentage of missiles in a stack thereby breaking up a swarm and giving anti-missile defenses more time to target them? One problem I see with that is that it would apply to small salvoes as well perhaps making missiles under-effective. Another potential thought problem is that if it was cheap to deploy in quantity missile stacks would get sub-divided until they were individual missiles.
Another idea I'll throw out is area effect missile defenses that destroy more attacking missiles the denser the attacking missile swarm is, but doesn't take out an entire swarm in one shot.