For starters, this would be great!! The design possiblities and introduction of resource management are a great great great idea!
You could make the "missiles" have all sorts of different modifiable attributes, like different speeds, different ranges, etc. by introducing different components. Combat only engines (ie various levels of afterburners) would keep the missiles from zooming through wormholes and across sectors. Higher speed engines/aftrerburners could use more supplies, giving a shorter range for example. Later technologies could allow for improved engines/afterburners and eventually very expensive (and gas guzzling?) engines that would have normal movement, letting missiles move across systems and through worm holes. This would allow a player to essentially enter combat without entering combat!
Now missile cruisers have an entirely different value

(I'm a missile freak, but I'm always disheartened by the strength of my enemy's PD weaponry. In the same breath, I wouldn't want missiles to become too strong).
Some players will design missiles with extra supply storage to reach across the entire combat screen, while others will let loose a volley of short range, high velocity missiles, while others will push slower, high yield "turtle missiles" out of the bomb-bay doors. Some will opt for the expensive missiles with normal movement Ratings, while others will go for the cheapest drives possible.
As far as the "fire em all at once" problem,
i) can't you limit the number of drones launched from a "drone bay"? (I don't know, cause I don't have gold... yet)
ii) if you can launch a swack of missiles (but not all) in one shot, I figure that's okay. The player will now have to deeply consider whether or not their ships will survive combat. If not, fire em all! If so, then they'll need to apply restraint.
iii) as to missiles taking out their primary target, and the extras going after secondary targets... I guess everyone will just have to be careful as to how many they drop over the side
Edit: oh, maybe you could make components that can fire only at certain targets. This way, you could design a missile that only attacks ships. Now you won't harpoon that planet by mistake. Sort of a hardcoded smart missile if you will.
My Last comment for the night. Missiles cannot attack satellites right now. To keep this important game balance, I think it would be important to only design weapons that can attack ships/bases/planets for these new missile types.
Ciao all
Good night
[ June 14, 2002, 07:42: Message edited by: jimbob ]