I remember reading some Dev comments that the current system is working as intended and they aren't planning any changes. Increasing your bulkhead armour just increases the durability of the actual hull, it doesn't in any way reinforce the sub components, they are all exposed on the wrong side of the armour.
Personally I think if you were to put some more armour on your ship it would be over the more vulnerable parts, rather than on the armoured parts. Its been a while since I bothered with anything but lightweight bulkheads, and I haven used the other armour upgrades at all.
I assume that the thought process behind that is the whole idea that in order for your components to be made available for destruction, you have to take someone's shield down first, which I could follow if the whole shield system tweaked different altogether.
Having the system pips influence the recharge and regeneration rate of the shield instead of its actual strength might be a good start, because the values that some ships reach is just ridiculous and it scales out of hand that way. We already have like 3 proper tiers of ships (4 if you include the starters) and the last tier has over 7-8 times as much shielding.
If the fight was more like:
Get shield down
Plant to ~80%
Get shield down
Pant to 50%
etc.
Or something similar it would make more sense.
Right now it's just: Get shield down -> win, because the recharge time is humongous
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