Another idea, hope you don't find this annoying of me
For capital ship missiles:
Weapon Seeker Tonnage Structure Formula := 10 + (([%Level%] - 1) * 1) + (Get_Empire_Tech_Level("Armor") * 10)
This would provide missile armor (this doesn;t cover the other kinds of armor though).
Also, the damage a missile causes could be affected by the warhead tech level.
These arn't really PD fixes, but it might be nice to have some of the components affected by other techs.