An idea:
To make area defense more viable (especially with the removal of laser warheads, which was the only practical use of it before), make it avoid range drop-off penalties. The way I'd see this most naturally happen is if you can flag BFCs for PD during design; this would give them flat accuracy across an envelope defined by the range parameter, but restrict said range and only be useful to fire at missiles.
I don't really like exception rules. If I can accurately hit a missile at long range, why can't I hit a larger, slower ship?
I agree, so thanks for forcing me to do a little more work fleshing out the idea.
First, it comes from a place of PD being really weak, compared to AMMs, once you get to inertial confinement fusion, or so. The fix to tracking bonus might already change this balance significantly, as might your idea of removing agility from missiles entirely, if you've done that, so it might not be needed.
However, assuming the balance is still substantially the same, I like the idea of rectifying the balance by making PD more flexible than it currently is rather than just boosting stats. Flexibility opens up tactical possibilities, and I believe that flexibility could easily be represented by expanding the effectiveness of area PD, having knock-on effects with various formations and so forth. Area PD in its current incarnation is really weak anyway, since you're always taking an aim penalty compared to final fire, which in turn means you're incentivized to just keep all your ships in one big TG until the enemy is out of missiles. Breaking that incentive leads the way to interesting formation tactics.
But that's not what you asked. How to make this make sense without feeling like a carve-out? A couple of proposals.
1) Make area-PD specialized BFCs capable of targeting ships as well with the same lack of penalty over their entire range. However, APD-BFCs would have extremely restrictive range compared to regular BFCs - still more than final fire, but low enough to make you want regular BFCs for offensive use lest you be hopelessly outranged. This can be justified by saying range is sacrificed for target awareness, or whatever the appropriate term would be. both new APD BFCs and normal BFCs would be capable of final fire PD without penalty.
2) If I remember correctly, missiles are already different from ships in that they used some sort of 'solidified sorium substrate' for fuel instead of the usual liquid sorium (or sorium-enriched LH2). You could say that this much more intense transNewtonian reaction pushes the missiles deeper into the aetheric fluid than ships can go, which in turn leaves a characteristc signature which is easily tracked by a system tuned for it. Much like how we use LLLTV cameras to pick up faint light, but a regular camera is much better at normal light levels because they swamp an LLLTV sensor.
3) (tongue-in-cheek) All transNewtonian civilzations discover and then sign, via their original transNewtoninan Elements research, a war rules contract with the Q which requires them to put IFF transponders on all of their missiles, along with other wartime protocols. Failure to follow these protocols results in John de Lancie personally revoking their TNE privileges. APD BFCs are tuned to read these IFF signatures whereas regular ones are not.
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However, the number of layers you have is your denominator while your Stealth Armor Tech is your numerator. So Five Layers of Stealth Armor at Stealth Armor Tech - 1 will give you a 1/5 reduction on whatever you mount it on. So you're 5,000 Ton ship, assuming it was already using 10 layers of normal armor, can have Stealth Armor fitted to render it as a 4,000 Ton ship. That's because for every 1 layer of regular armor Stealth Armor requires two layers, making it twice as heavy. However, since it uses your regular armor as a base, you can upgrade your regular armor tech to make it lighter.
