How about just disallowing the waypoint missile swarm entirely? That would seem to resolve a bunch of issues. Otherwise I expect it'll become SOP since there seems to be little down side to it and a lot to gain by forming a swarm.
I don't want to take away the ability to fire missiles at waypoints because it is useful for other reasons as well, such as firing drones or aiming missiles at the path of a contact rather than directly at it.
I have been reading up on electronic warfare lately so a future version (but not v4.0) could have systems along the lines of the following:
1) Jammers that can jam all active sensors and fire controls of a particular resolution within a specific area. This will affect friendly ships within the same area as well.
2) Jammers that jam a specific hostile active sensor within range of the jammer
3) Decoys that will have a chance to distract self-guiding missiles within a set range
4) Decoys that will appear to be ships to enemy sensors, or flares to generate thermal signatures
5) On-board blip enhancers to make targets appear larger
6) Some form of chaff to block hostile fire control against a specific target
7) A Towed decoy that exactly replicates the signatures of a particular ship
8) Specialized passive sensors that can detect the lock on of hostile fire control systems
These systems would replace the current ECM. ECCM would consist of improved sensors to burn through the jamming or be able to figure out which are the decoys, etc. This is all in the early stages at the moment though.
Steve