An indestructible capital ship class, you say?

[Zynth]

It would be interesting if they had "subsystems" where if you damage a certain part, it's overall efficiency goes down.

Eg: If you shoot off the engine, it slows down.

But that's a tad of a far shot, perhaps try a core nerf instead?

The most basic way would be to implement the technerf system.
Certain parts would be given the same status as an ID or so. Shooting it off removes the part and results in a core nerf. This can be continually done until the ship becomes useless.

Or something like that....

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