May I suggest with tying different subsystems to figthers be limited, not completely tied?
Example...
Have 4 classes of systems...
Class A: Lightest fighters
Class B: Space Superiority fighters
Class C: Heavy assult fighters / light bombers
Class D: Bombers, heavy transports
Changable parts:
Engines
Shields
Reactors
Primary systems
Components of Class A:
Reactors (1 slot):
Reactor
Heavy Reactor (5% slower ship)
Shields (1 slot):
Pierce shields (against piercing weapons)
Energy shields (against primaries)
Collision shields (for kamikaze attacks?)
Missile shields (against missiles)
Beam shields (protect well against AAA beams)
General shields (about average)
Englines (1 slot):
Light engines (25% less power draw, 5% less maneuverability)
Medium engines (Normal power draw, normal maneuverability)
Heavy engines (40% more power draw, 10% more maneuverability)
Primary systems (1 slot):
Light weapons (25% less power draw, 20% less refire, 10% weaker shots)
Weapons (normal)
Heavy weapons (40% more power draw, 10% more refire, normal strength)
It could add up to

of confusing options...
Class B would be similar... 2 shield options.
Class C would be double-system, except only 1 reactor.
Class D would be ultra-heavy stuff, up to 2 reactors, 3 shields, and 2 weapon systems.
Just think of the energy draw... perhaps add a "Overburner", sort of a "Afterburner" but can be sustained for three times longer... and doesn't rumble the ship. Link that to afterburner drain... only when you max out engines can you keep that speed sustained.
Also, when you put all energy to shields, your specialized shields become 10% better then normal shields and keep their special. Normal shields would become similar to specialized systems, but has a 30% boost.