I really really like the idea of capital ships, and to make all the customization and determining easier, to create balance (I am not good at equations unless I work them out myself and take the time, so this is just a quick assessment)
For every point of defense, 50 maybe 75 M
For every point of offense, 50 maybe 75 E
You cannot upgrade or customize basic forms, such as the Hawks or the other craft, however, you can create your own ship, of sorts, to act as a capital ship. In terms of buying them, just give them the name "Capital Ship" and give the player the ability to rename it once he buys it. And any number of capital ships can be placed in a group. Obviously, making this setup would require alot of time and effort to code and implement, maybe introduce it as a special for the grand opening of a future round?
Also, capital ships, maybe one can designated a flagship?
And back to customization: the capital ship can be the only one to customize, or maybe the lower two or three tiers (like the ones you unlock at the current game's level 4 war?). And also implement that other system you mentioned earlier in the post... I talk too much I know, but I just really want the implementation of customizable flagships.