@DatonKallandor: Thanks for posting up those reload numbers. Could defnitely see it working, like I said, but I'm just not a fan of long cooldowns myself. Sometimes cooldowns are hard to avoid design-wise, but it feels like if you've got enough of them, managing them rapidly becomes the name of the game. It does make things easier for the AI to work with, as the cost of getting a "should I launch missiles" decision wrong is lower.
As the player, though, you'd probably feel like you have to wait out cooldowns to engage optimally. Peak effectiveness seems like it would combat this, but it doesn't tick down when there aren't enough enemies around. So, if you're in a Hyperion, it seems like an optimal way to fight would be to teleport in, unload whatever missiles you've got, then teleport out and hide in a corner somewhere while the missiles reload. Could be addressed somehow, but that's just the most egregious example of the pattern of play I think long cooldowns would encourage. Plus, as I mentioned, I like the decision layer that having truly limited missiles adds.
@Wyvern, Megas, Thaago:
Bumped up Autopulse damage to 150, and flux use to 125. Hopefully that'll be enough; I don't think a drastic change is called for here, but in my experience, the weapon did feel weak-ish. It's not supposed to be super-strong, with efficiency being the main selling point, but even so, it's still a large slot you're using.
Also added the PD tag to the Proximity Charge Launcher.
... and while I was at it, set the Apogee's Sensor Drones so that they can't free-roam. Been meaning to do that for a while.
(I'd like to take this opportunity to say thank you to everyone for all the detailed and thought-out feedback. I very much appreciate it.)