What if...

[Armageddon]

Possibly only be able to disable the engines on larger ships then? Such as BC upwards. That way you could hamper their ability to fight by completely taking out their maneuverability. But as i say there would have to be an easier way to repair than to scuttle the ship. Possibly an undestroyable backup engine that only moves the ship at a speed of 15 and no cruise. (A bit of an alteration would be required to large ships to make them not go over 79 speed but it wont be too much trouble to implement. (If my knowledge is correct on this bit). Would be quite comical to see a cruiser on backup engine trying to flee a fight.

I believe all equipment needs an HP nerf so that they take damage on fighters from Sunnys (blast damage) Same with novas for caps.

For the caps it would add a more RP standpoint of disabling a capital ship instead of destroying it to learn its secrets. Have fighters attack the turrets while a heavier ship takes down the engine and all other equipment leaving the ship almost dead in space. (Except for the before said backup engine.) Leaving you to RP an docking maneuver with the disabled ship and have a RP fight inside it.