Hey guys I was thinking of something to go along with the mobile defense and ships that build ships. I am new to the modding community here so please forgive my ignorance.
Would it be possible to have one constructor ships who's special abilities would be to spawn the capital ship facility and the frigate facility? However to keep from spamming a hundred facilities the constructor ship would actually be spawning a variation of those facilities that take up a small amount of unit cap.
Right now, that is the hard part, 
Trying to get one ship to create another, i havent found a way yet. Both the CapitalFactory and the FrigateFactory are PlanetModules and as such are tied to the planet, and i havent been able to get either to launch from a ship yet.
One of the other modders, and Blair said it could be done, BlackSeraph did it, but i havent seen how. And there was mention of having ships like the frigates and capitals that launch fighters/bombers, that a substitution of a special modified fighter/bomber squad could be used to call the meshes for the ships you are looking for. I haven't tried this yet, and with 1.1 my modding ability is zero, until i can get text versions of the ship and ability entity files to work with. I have heard conflicting things about the convertdata.exe, so i am not sure if it addresses just the ship files, and not the abilities, or if the new convertdata.exe will handle all of it no problem. Once i can do that i can try to see if i can make one ship create another. And if it works, haha, if it were only that easy, then i could fill up the modified squad file with different ships. But we shall see.
As to limiting spawning? perhaps it could be done, as you say, by having it cost a certain amount. But at this point im not even there yet, so i dont know. Once we actually get them to create ships, then i can see how to limit them. I believe frigates and capitals have a cost associated with them, but i am not sure i saw a cost or slot count for the squads since they are associated directly with the ship or hanger that produces them.
Then each of these specialized facilities could either have their own fighter compliment, or modified fighters that would consist of defense platforms or something along those lines. This would lead to people actually creating ship yards near a star (central part of a system) to quickly respond to problems in system. Or even setup a stronger ship yard at planet since these modifed shipyards would not use planet slots.
Actually what you are proposing is exactly, i believe, what Entrenchment does. So if you wait just a bit, you can get a developer made entity that does exactly that. But much more professional than some little home made mini mod by me.
This would allow allies to setup ship yards together, so alliances would be worth more so you could concentrate your defense or shipyard setup in enemy territory. This would also give the enemy a place to strike.
Entrenchment again.
The other thing I guess you could do to help balance it out and have already done my self is to make capital ships only use 25 ship cap instead of 50. To me this makes them a little bit more worth their weight because in mulitplayer hardly anyone ever uses cap ships anymore. Yea its balanced where a fleet cap of frigates vs same cap of capitals it is balanced, but they are capital ships, you WANT to build them and see more of them, their CAP ships.
Just a few suggestions, I am willing to help you guys out if you need it.
