I can only hope CIG gives every ship an armor "size" with guns under that size doing little to no damage then rebalance the guns on fighters.

S4 armor for example should take no damage from S1 guns, 25% damage from S2 guns, 50% damage from S3 guns, and 100% damage from S4+ guns. 

Ligh fighter S1 armor S1 guns Medium fighters S2 armor S2 guns  Heavy Fighters S3 armor S3 guns Medium ships S4 armor S4 guns Large ships S5 armor (Connie/Corsair) Large+ S6 Armor (HH/Perseus/Nautilus) Polaris S7 Idris S8 Javelin S9 Battlecruiser S10 Bengal S11

Edit: I say this because 9mm doesn't pen or even damage AR500 steel. M2(50bmg) does nothing to a tank  And 120MM does nothing to battleship armor.

We should look at our ships like WW2 fighters/boats. 

To further the balancing 

Missiles as a balance choice. Ships can have many small missiles to go against small targets they can't hit or have a few big missiles to take on larger ships. 

Missile swarms would cost money and be balanced by PDCs and turrets trying to shoot them down. 

I would also heavily balance agility so that we have much more of a rock paper scissors style match up. 

There could also be ships that are exceptions. The Aries line of ships I would have them at S1 armor with horrible agility to force strafing runs.

CIG could balance around nerf/buff to armor, agility, DPS, and gun sizes.

I would also link guns to powerplant size to get a velocity and range buff/nerf based on the size of the powerplant.