The simplest way to make the missile/pdc situation more balanced is to remove the built-in BONUS to hit from the PDC. They have a 50 percent modifier in the components.txt files, so as things are now they are at 100 percent to hit at full range of five. Remove the 50 percent bonus and they are only 50 percent likely to hit at full range. Unless you have Combat Sensors, and then the CS bonus is added to your PDC just as it is to other weapons. So, you'll actually see pdc MISS once in a while. Amazing!
Now that's realism. I also wish MM would add some way to modify the 'ecm' value of seekers so you can have better protected missiles at higher techs but this is a start. Another good change would be if missiles could actually MISS themselves once in a while. Missiles and mines need a real 'to hit' chance instead of this infallible damage.