Walt Aside from what's already suggested on the trello:
One idea would be a cloaked mine factory. Mines are launched from the missile launcher, stop after a brief distance, then cloak and wait for an enemy ship to come near. When an enemy gets within a very close range the mines decloak and accelerate towards the enemy. If the enemy gets far enough away from the mines they stop chasing and recloak. Sensors would allow you to detect mines within a moderate or small radius, and PD could target mines. Mines would be visible to friendly ships. If a friendly ship hits a mine, it could despawn/pass under the ship/deal friendly fire/get pushed out of the way.
Limpet missiles could add an interesting mechanic. Limpets would latch onto an enemy ship and maybe could 1) explode after a delay, 2) slowly drill into an enemy and then explode, 3) weigh down an enemy/thrust against an enemy, or maybe even do something else exotic like hacking or boarding. Limpets would still be vulnerable to PD while latched on, but you'd probably need another ship to fly near and get an angle to "clean off" all the limpets. If they hit shields maybe they would penetrate, maybe they would bounce off (with a chance to impact somewhere else), maybe they would explode.
Siege missiles/cruise missiles. Extremely long range, excellent guidance, fast, powerful, high-damage, all that good stuff. To compensate, the factories would be extremely large and heavy (increased density maybe?). Good for space stations or big slow ships, but far too heavy for use on a kiter. If you use these you condemn yourself to a slow movement speed, but if you wanted to make a space station anyway this would be the perfect thing.
Unguided, short-range torpedoes/rockets could also be interesting. These would have a focus on burst damage, with expensive, slow-producing factories, but with large amounts of damage in each launcher when completely full. Visually I think it would be cool to have 2 or 3 rockets per missile tube, but the same thing could be accomplished with 3x damage and 3x durability on each rocket. Probably a lot of random spread when they launch. Basically the torpedo suggestion from the original post.
Other ideas: airburst missiles, anti-missile interceptor missiles, shaped charge/bunker buster missiles, AI missiles that try to avoid PD coverage (possibly requiring sensors, a larger control room, or some sort of "computer core")
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Crew reload efficiency (damage per part) vs missile part production time could be tweaked for each of these to make things interesting. For example, maybe rockets are slow-building but can be reloaded quickly, so I build up a stockpile while bombarding the enemy with faster-building siege missiles. When the enemy gets close, I swap to rockets and rapidly drain my stockpile. Reload efficiency/damage per part also impacts storage efficiency, which could be used to make storage more useful.
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In general though, I think it's important to find a good balance between current missiles and PD before adding more missile types.
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Mc2 normally only Battle helper results count, no manual control against AI
That's what I did! I don't have the patience to control a PD cube for the half hour it took to destroy the U.