My idea for fixing point defense targeting:
Make it so that when a ship is going to target and fire a point defense type of weapon at an incoming missile or bomber, run a check to see if anything else in the fleet already targeted that missile. This would require that the missile or bomber get a new tag variable for something like "Is_targeted" or something like that. When a weapon fires on this entity (missile or bomber) then the target has this new variable set so that other ships looking for targets know to skip that one. So when a ship is going to target and fire a point defense weapon, grab an array of all targets within range, sorted by closest target first, possibly even sorted by closest+missile type. If the first target it seeks for is already being targeted then skip to target B, then C, etc. Maybe truncate the array with only 6 choices or something to keep calculations down. If the ship reaches the end of the array of targets and all are already targeted then choose any of the choices within the array at random. Experiment with how deep the target array is (4 deep, 6, 8, 10) to get the right feel for effectiveness but limiting how CPU intensive it is. Perhaps even have a secondary array that specifically filters out the closest 24-36 targets and populates the array of targets from that next step back from the front wave, then make a point defense weapon randomly choose to check primary array or secondary array in order to spread targets out even more and to combat how bunched up both missiles and flak frigates in fleets can be.
A change like this should help point defense weapons target far more effectively and more apart from each other, instead of locking on to the same target for everything. Perhaps to make calculations run even more efficiently, run a proximity check to other ships and if too many ships are stacked on top of each other then group pairs of ships as a single targeting entity so you end up cutting down on half the calculations without affecting the firing too drastically.
Hope that idea helps get the creative juices flowing on the dev team 
