@Walt
I'll weigh in.
My stance on missile/PD right now is that it's a boring and unfun dynamic.
When I build a ship, I usually include moderate PD. I put a few wherever I can squeeze them and say, "That should be enough." Then I go into a fight find out if I really had enough. How much is enough varies wildly. There's just no telling if you have enough PD or too many until you get in the fight. So there's no real engineering challenge there, just a goal to meet a basic requirement of every ship: "I'll add some PD, I guess." That's no fun.
Part of the problem is how missiles work. They have 100% accuracy given no ship movement, and they have the longest range. Which means the only counter to them besides boring PD is just staying out of range (and thus out of the fight). This is boring because it's not a tactical choice; it's just fight or run.
Of course there are other ways to defend against missiles; shields, armor, and movement. Shields really aren't that good against missiles, since the missiles can hit through them if the shield arc is close to parts. Shields also go down pretty quick to missiles - large salvos can bust right through. Armor is armor, no explanation needed. Now movement is great! You can ruin an enemy's initial missile salvo if you just run from it. However once the fight is engaged, it's just an endless hail; movement will only help in that it can give PDs more time to shoot if you strafe away from the missiles. Even then the situation is still a question of whether you have enough PD.
So what the missile/defenses meta needs are:
1. Engineering choices (beyond, "Should I add more PD?").
2. Tactical choices.
I don't have any ideas right now for the engineering part. The current engineering choice of whether to add PD or not is, "Can I spare the surface area here, or would I rather have more weapons/armor/shields/thrusters?" That's a choice of necessity, and we just can't know how many PDs we'll need. I think a targeting computer just makes PDs even weaker than they already are. Basically it makes PD a larger part, albeit a malleable one. Larger PDs makes them less likely to be used in quantity, making dedicated missiles ships more likely to be able to obliterate their opponents.
I do have some ideas for tactical choices.
Make PD arc narrow, make them really accurate, and spray a lot of fire. A bullet hose that sweeps away lots of missiles easily with a long spray. This will make PDs really good at shooting down missiles, but you must rotate your ship to properly spray them down. A flaw in this style is that the decision would only matter against large salvos. There would be no way to react to continuous missile bombardment.
Weaken PDs, but add the previously suggested ECM functionality to sensor arrays. When activated, sensor arrays consume all of their stored power to create a field that inhibits missile guidance for the currently targeted enemy for 5-10 seconds. I would hesitate to make ECM usage work like boosters because the drain can be overcome, leading to ships that can keep their ECM active permanently. If a player wants more ECM time, they would have to place more sensor arrays. Having an actively-used defense to counter missiles adds a little micro and some timing considerations to a fight. ECM might also reduce vision radius of the targeted enemy to half of their current max, effectively halving enemy weapon range for the duration. This makes it useful for more than just missile defense.
To fit together with ECM, PDs could be changed so that they can only kill one missile per second, but they would also have a high success rate (no missing) and lower power drain. This would make them strong against sustained bombardment, but weak against large salvos. Against a salvo, they wouldn't have time to shoot it all down. For this to work, you would have to make it so that PDs coordinate - one PD per missile so that multiple PDs don't target the same missile.
This ECM/PD setup would also encourage a tactical choice for the missile guy - should I do sustained fire or should I hold fire and build up a salvo?
Also, maybe take Verania's suggestion and allow PDs to affect physical projectiles like cannon rounds (though I think they shouldn't destroy cannon rounds, just divert or slow them). This adds to PD usefulness.
These changes diversify missile defense, add tactical choices that require observation and timing, and have the potential to make the defenses useful against more than missiles.
Note: I don't suggest option 1 and 2 together - just one or the other.