As I said though, I see the potential in the changes. In fact you basically turned missiles into what I described above as MIRVs. Less damage than a normal missile (you reduced their damage), but at least some of them get through even the thickest PD screen (you did this by weakening PD).
My problem is that the missiles that get through are still causing too much damage. You cut their shield damage and area damage in half, but I feel that's not enough, not for how many missiles are able to now reliably cut through even what was previously considered a strong PD screen.
I highly suggest returning missiles and PD back to the way they were until new complimentary systems can be implemented to better balance the missile conundrum. Because what just happened is just a huge universal buff to missiles. Where previously a missile alpha strike heavy ship, you could survive that alpha strike, and then have enough PD to handle the trickle, now you can't handle the trickle, and that trickle is an unstoppable river of damage with ships who have a crazy amount of missiles.
How would new systems fix the issues?
Well you would have purpose-built interactions instead of trying to jam a one size fits all solution into a single weapon (missile) and single counter to that weapon (PD).
Currently, missiles are crazy powerful, but excellent PD can shut them down from crazy powerful into pretty much nullified. That's not the best interaction, but let's move on.
Add a new missile type into the mix, the MIRV. Smaller, weaker, but designed to at least get some missile damage through the thickest PD swarm. Now your normally great PD defense has a rock paper scissors relationship. Beats normal missiles, is beaten by MIRV missiles.
In a pure DPS check, a normal missile is a far better option to use than a MIRV, but a MIRV makes up for this in those cases were a normal missile wouldn't ever reach the target.
Now you need a new PD type to compliment the normal PD. And this new PD type will also answer the problem of the Equalizer ship too.
The FLAK PD. Instead of firing a machine gun spray, which can't keep up with a massive swarm of missiles even before the PD nerf, the FLAK PD throws up bursts of shrapnel, and this AOE of shrapnel destroys missiles in a good radius, taking out huge swaths of missiles at once. FLAK PD is too big and expensive and unnecessary on small ships, because small ships would be using 1-3 PD to fully stop damage from 1-2 missiles, as the game is on non-dev. FLAK PD is meant for much larger 1M-5M ship sizes, and with enough FLAK PD, they are designed to combat against absolutely overwhelming amounts of missiles, like the Terror or U ship can bring to bear.
But FLAK is not without its flaws, If you make it big, like cannon sized, and require ammo, a FLAK gun becomes a liability against a direct fire ship. Focus fire, something you can't control on a missile only ship, can select target FLAK and FLAK ammo bins, for example.
As the options only grow as more options are added. A torpedo missile could be good against FLAK, but weak to normal MG type PD. A torpedo missile would be like a large single missile that is extremely durable, but not as swift or maneuverable as a normal missile. So it's tough enough to ride through the FLAK cloud and connect to its target, but flounders against small swift ships and concentrated MG PD fire.
TLDR: Point is, the missile and PD are in good place, as the baseline for missile and point defense type interactions. Tweaking their systems to values to try them to get them to a one-size-fits-all solution is never realistically going to work because design in this game covers an incredible spectrum of possibilities, from the little pincer to its surprise missile on a 100k frame to the gargantuan U ship just covered in missiles, and then beyond to modded ships. There's just too much. What's needed is more types to compliment and supplement the baseline interaction. FLAK PD, MIRV Missiles, Torpedo missiles, and hopefully more cool stuff!