A new variety of weapon that can be researched and built alongside energy weapons, it would be a little different than how it works now. Instead of adding to your attack stat directly, it has a value completely it's own. To fire, it would have a new button on the battle tab. To limit it's use, you would have to load your hardpoints.

Let me re-iterate. For example, you build a Heat-Seeking Rocket. It takes up 5 space, has a damage of 10 and has two hardpoints. It also uses 25 Dynite to load each hardpoint, and a timer that has to cycle before you can reload again. You can choose how many hardpoints to load each cycle if you need to micro-manage your minerals, but the timer would be uneffected by that choice. Tese weapons would have a higher dmg-space ratio than existing beam weapons, but a lower limit to how many you can have onboard. Say, 3 mounts (the above example would be one mount with two hardpoints, not two mounts). This also gives some meaning back to the low-end minerals.

This could also be applied to planet tech, a defensive installation that fires once during an assault, then spends time to reload.

Did a little bit of further thinking about this, and came up with aa few more details.

Missiles would be in alternating tiers, Missiles/Torpedoes. Missiles guide in on a target's heat signature (Energy recharge rate), and torpedoes it's radar signature (deck space).

Defense is not used, rather your stealth plating decreases a missiles odds to hit, and jammers for torpedoes.

So, your saying that missles and torpedoes would be single-use attack buffs that damage based on the opponent's cloaking instead of defense?

Yes, single-use, reloadable attack buffs. The chance to hit would be based on the target's cloaking score, depending on the correct type of cloak per missile type. If you're firing torpedoes at a ship equipped with stealth plate instead of jammers, you're going to hit.

As for damage reduction, we could use the ship's defensive rating like normal. We could do something different, as well. Instead of relying on the defense score to reduce missile damage, it could be based on the tech level and number installed for your hull plating.

I also thought of a missile tech tree...I think yours is better than me. I think it's a good idea, although you would probably need electronic countermeasures for defense against the missiles.

There's two reasons I went with the stealth plating as missile protection. If the missiles are said to operate on a heat-tracking basis (which is why I suggested that the faster the reactor charges, the hotter it gets, thus a more likely target to strike), then the stealth tech can be said to help mask and dissipate that heat more effectively. The other, more practical reason is so that there's no need to invent yet another line of technology to go with it as a balancing agent, just use tech that's already there. Remember this is different from jammers acting as torpedo defense.

I mentioned earlier that using the hull plating itself to step down the damage was an option. Let me elaborate more on what I meant. Let's use Whipple Plate as an example. It's a tech level 3 ship part, so let's give it 5 points of missile dmg reduction. Now it also comes in three flavors, so let's make those different levels of hull plating be worth 33% and 67%, respectively, of the value of the full 5 point bonus. Finally, if you have two pieces of lvl 3 whipple plating installed, that would grant you a bonus of 10 points of projectile weapon protection, be it missiles or torpedoes.

you wont need a separate tier when you could have special artifacts that do the same thing. i have suggested some damage causing missiles before. it would be nice to have the damage adjusted based on weapon tech etc. having them be artifacts would make them rare.