Alex, you've said these system can't be disabled, but can they be suppressed by other subsystems?
I vote for radar jammers and stasis webifiers next as ship systems!
Only if I can get my energy neutralizers and tracking disruptors... and cloaking device for my pilgrim
Hey! Both of you! It's my ideas sent to Alex 100 years ago!
Tractor Beams - to catch ships and bring them closer to you.
Lockdown Modules & Stasis Webifiers - modules to slowdown/stop enemy ships.
Weapon Disruptors - decreases weapon range and accuracy.
Stealth Devices - hides ships from radar, but not from eye.
Cloaking Devices - hides your ships from enemy. Uncloaks (or not, depends from device) when starts shooting.
Scanners - to scan the ships for additional information or for cloaked ships.
Scramblers - to resist scanning (scanner strength vs scrambler strength)
Missile Jammers - jams the missiles from course or even redirects it back at enemy.
Damage Over Time - something like acid on the ships hull, or sprayed in space waiting for victim.
Remote Repair Systems - that can temporary fix ships hull.
Energy Focus Systems - ship A transfers its energy/flux regen to ship B to increase its weapon output.
For example:
Burn Drive and Combat Thruster could be countered by Stasis Webifier & Lockdown Module (disable main engines, but allows rotation).
Weapon Disruptor that can affect weapons accuracy and Targeting Module that can suppress or decrease effect of Weapon Disruptor.
Stealth Device that will hide ship from tactical display and Combat Radar that will reveal hidden ship and increase detection range.
Cloaking Device that will make ship invisible, but can be disrupted by Combat Sensor and damage from weapons of enemy ship.
Scramblers that can hide info about your ship like damage and what weapons installed and Scanners that can suppress Scramblers.
Missile Jammer unlike flares can redirect incoming missile to another location or back at enemy ship.
Teleporter and Jump Drive can be countered by Warp Disruptor, that within limited range can block them & etc.