I've done some testing with Missile Prototype 5. Here is my feedback:
EMP's seem like an effective counter to PD, given their speed and blast radius.
It now seems to take 4 point defenses to fully counter 1 missile launcher. This will force people to cover large areas of their ships with PD's. What if PD's were powerful like in 14.4, but became less accurate when tightly packed together? You could say their radars were interfering with each other. They would be at 100% when at least 4 spaces apart and effectiveness would go down if placed closer together. That way people could still use lots of armor as their exterior. You could also increase their energy consumption and price if that wasn't a big enough nerf. On another tangent, I saw two other ideas I liked in the comments.
Dalas120 Maybe have PD fire in bursts? That way there would be fewer projectiles on the screen at once, and PD keeps that rapid-fire machine gun feel.
and
kieffer5101 i had an idea recently, what if when missiles/mines get shot down the explosion that they make or, at least have a chance to explodes other missiles/mines, possibly creating a chain reaction.
All the changes to mines are great. Mines are now much more fun to use. It is really cool to see them bouncing down the side of a ship, but unfortunately fast ships can bounce them away before they explode. Minefields should be an obstacle you have to slow down for, not something you can ignore by going super fast. One way to have your cake and eat it too would be to make mines magnetic. Mines would not home, but become magnetic when a ship strikes it. The mine would stick to the side of the ship while rolling down the side, blinking ever faster until BOOM! I would also like to see them blink brighter when counting down. As for preventing players from building boxes of mines for ramming, I'd say the best option would be to have the mines deactivate and disappear if they touch another mine for more than a second, but only while not counting down. I think that is a better than making them disappear if they touch a friendly ship, although that is also a fine option.
The smaller Flak Batteries are easier to place and shield. The 45 degree firing arc is a great improvement. The gray flak projectiles are hard to see against the black. I also liked Vess's idea
Vess I still think Flack should AOE intercept. Like missile command on the atari. 
That would also help with performance since there would be less projectiles.
Nukes not being able to home at all is a problem. They work okay as long as your ship approaches head on and the nukes fire as soon as they are in range. However, if you put your nukes on the side, they fire too early as you rotate to put them on target. This causes them to all miss. It also feels wrong considering all other missiles home in.
Another solution would be to make a rotating nuke missile turret, but that makes them essential a really powerful cannon.
Missile factories using more power seems like a good move.
