Below I ignored personnel, fuel, missions for now. It's only about components (mechanical stuff you install on ships).
Production & budget
I think there should be two completely separate production facilities: shipyards (produce ships) and factories (produce equipment you install on ships). It would give more control to the player (on the ratio of ships to equipment) plus it's intuitive and realistic (orbital shipyards make hulls and ground factories equipment to install on these hulls).
Also, when idle these should produce civilian goods (actually, I feel the player should be encouraged to keep like 25% of these permanently idle for purpose of supplying civilian sector and switch to 100% only during wartime). Anyway, they player would not be punished for not having a perfect ratio of shipyards to factories.
As for budget, I think there should be a numeric [$1,000,000] general military budget (production of new stuff) and then a percenatge [40%/60%] budget for shipyards & factories. So, when there is lack of resources the player can tamper with just the general military spending slider while the ratios of production would remian constant.
Also, since factories & shipyards can produce civilian goods, whenever you have too low budget to use these at full capacity these would automaticly produce resources (civilian goods/income) which later allows you to increase the military spending (a nice self balancing system without micromanagement).
I'm not sure, I was thinking more of mutually exclusive choices (if you installed heavy armor there is not enough room for weapons; besides, if you have heavy armours you might want life pods as well I suppose), it might be more fun/reasonable this way... On the other hand having slots and saying that Hull type X can always have at least one shield and it does not limit the number of other components is fun too... Maybe some mix of these (tonnage & slots)?
by selecting core component, offensive, defensive, and luxury/misc. supply priorities. The automation takes over and the player uses whatever he gets.
Also, I was thinking of not having priorities for all things (if the choice is obvious).
For example, reactors (delivers energy). These could be fully automated, like if a ship has lots of weapons the AI installs a better reactor, when it has too much power it uninstalls current reactor and installs a weaker one instead (the AI would try to always install the weakest reactor that meets the energy criteria).
Or (more complex, not sure if it's good) boosters. The player would have a slider "optimum speed" for each fleet. The AI will try to add to that fleet ships that meet this criteria and if the ship is too slow it would add engine boosters as the first priority (overriding other priorities like weaponry and armour).
With this system I guess there would need to be some feedback system. So the AI can report to the player "we are having not enough reactors of power 40 or higher" or "more engine boosters would be nice". Then the player could adjust production priorities or budget or build more factories or order researching better reactors.