Currently, weapons are either labeled as "Point Defense" or not. Weapons best suited for PD are designated as so, but weapons that are less-suited to the job have no option of being PD weapons. While this is a quite reasonable system to prevent missiles from being ignored/shot at by everything, it doesn't allow the player to change the designation in-game.
My suggestion is that PD weapons are designated in the "Weapon Groups" option. It could be renamed "Weapon configuration", and each weapon could have a toggle button for PD designation. Weapons that are labeled "Point Defense" (when PURCHASING) are designated as PD by default, for simplicity. Also, much like selecting weapon groups, shift-click would change designation for all weapons of one type (let me know if you think it should be all weapons of one weapon group instead of type).
This freedom would let players use, for PD, weapons other than the few that are set as PD (needlers might make good unconventional PD weapons). Also, it would allow for players to turn OFF the PD designation on weapons that they would rather have prioritize ships over missiles. As an added bonus, it would let people make zany choices for PD (such as Mjolnir Cannons) that would be hilarious to watch.
NOTE: This would most likely involve the change/removal of the Integrated Point Defense AI hullmod. Personally, I don't understand why we have pay extra to make weapons target missiles, when they can target fighters that aren't much larger.
EDIT: If you select "Other" in the poll, PLEASE post your idea! It doesn't help me if you don't share your thoughts!