I am curious about the reluctance to incorporate a fuel and ammo system into the game. Missile launchers need missiles, AMC's need anti-matter (or slugs, or whatever it is we shoot from them these days), beams need chemicals, etc. There should also be some sort of reaction mass for reactors and/or thrusters.
Instead of filling our ships with x-number of blocks to make it more powerful - the creation of a complex and modable system of reactors (power and shield) that relies on fuel makes ship creation a little simpler (create a reactor template that corresponds to a size of ship, load it into the ship when complete). That system space is now a new cargo-type block (fuel cell, ammo magazine) that holds the necessary components for the system to function. Ship size remains a limiting factor - a small ship holds less ammo/fuel, but might be more efficient. Also, a small weapon system can only expend x amount of ammo (weapon strength) at a given moment, and the size of the system also determines the speed of reload/recharge. The controlling weapon block (say, cannon computer) can be modified with a value (percent) that determines the amount of ammunition expended, and therefore the power of the system.
Reactors still play a role - being necessary to power the components. But instead of being the single limiting factor of the ship in the way they are now, a reactor system provides x amount of power to x number of systems blocks. ALL blocks now are assigned a controlling computer so that you can shutdown/turn on systems to meet your power needs. It should be feasible that a single large reactor that doesn't take up half the ship can power all components of the ship, or even a series of small reactors.
The key point here is the need for resources. This system should bring in a more strategic thought process in fights, but also make crew more relevant. Your highly skilled crew can make more efficient use of weapons and fuel, and a trained engineer could float power from a system you don't need to a system you are trying to use. Even better, though, there is a whole economy that is required to keep a large fleet on the move. A smaller ship can equip itself with a few salvage beams and keep floating, but a fleet or titan will need to suck up a whole asteroid field after they death star a world or station. You won't be able to just go around killing everyone, you're going to need some allies to trade fuel and ammo with, or some support ships to make it yourself.