As I understand it, AoE damage is a very binary affair. You make an impact, a radius is formed around that impact, anything within that radius gets the AoE damage. I feel this is problematic for a few reasons; weapons are either too powerful because of their AoE, or too weak because their huge AoE demands a weaker weapon. While balance can ultimately be achieved even with this behavior, I feel we can do better.
Instead of this, damage could taper off depending on how distant the point is from the impact. So if you have 100 AoE damage, and an AoE of 10, something that's hit at 9 units from the AoE would take, say, 10 damage (10% at 10%, a completely linear formula).
This would also have the effect of indirectly nerfing ships that have close weapons (see: the Junker) as their components are now easier to disable with AoE compared to other ships.
AoEs could be made bigger to compensate for this, but the biggest thing this does is makes AoE weapons harder to use. It is now demanded that you make an optimal shot if you want to damage multiple components. If you want to disable one component, you're going to lose out on damage to other things. This adds choice, which in turn adds depth.
And I think adding choices is always healthy for a game. What do you think?