The identified problem:
Shield resistance is a 100% hard BLOCK to enemy fire of all types. Thus every fleet MUST have some method to take down the maximum-shield resistance modules in the game, and every fleet MUST equip those modules wherever possible (at least one of them). Why is this bad? Because no-brain choices are no choice at all, and it reduces the scope for interesting tactics. Everyone is using the Heavy Shields, and everyone is ensuring their ships have those weapons that take them down.
Shield resistance is changed so that it becomes the AVERAGE shield resistance of all shield modules. This way you need to either really commit to a high resistance strategy or abandon it. The downside is that this negates the whole existence of the shield capacitor module which is designed to take advantage of the existing mechanic.
We nerf the non-shield damage capabilities of weapons with high shield penetration. For example heavy plasma has shield penetration of 27 but armor damage multiplier of 100% Arguably no weapon with heavy-shield penetration capability should do 100% damage to armor or hull as well. This would give you an incentive not to over-supply your ship with these weapons, as the initial shield-taking down is all they are good for.
We beef up shield disruption as a mechanic. giving the weapons that cause this a high capacity to disrupt shields, making this a more commonly used tactic, and encouraging people to attempt this rather than bother with cutting through high shield penetration
A totally new weapon. The shield penetration beam. A weapon which does no damage, but it does change the enemies shield resistance whilst active, effectively letting other incoming fire tunnel through the resistance and do shield damage regardless of their shield penetration. The plus side is this is another weapon we can give to maybe frigates or destroyers, encouraging the whole ‘combined arms’ thing. I could write code for weapons to prefer affected targets if their weapon could not otherwise penetrate.
I like the idea of #4 myself. Any thoughts? or indeed, better ideas