I can't imagine this hasn't been brought up, but two systems (one for ships and one for missiles) that actually increase the cross section/tonnage that comes back from an active sensor. Basically, being able to have a 4000 ton frigate appear as a 12,000 ton ship, or a missile/drone look like a ship. This might really cause havoc with the AI though, as I can't see it being very good at making decisions about if a decoy is a real threat or not.
Also, if you could just have the ability to move/change a way point and then actually have a missile fly to the new coordinates, you could basically command control drones and missiles. Once more, I am not sure if the AI could use this, so it might be unfair from a balance standpoint. With that being said, A4X has always been more of an RP platform, so it could be an option for players that wanted it. I know in old school AAR's there used to be a way to control command control missiles, but wasn't playing back then so I don't know the older mechanic or why it was dropped.