I would change the dice system, by decoupling accuracy from damage.
Like, the current red dice would be the accuracy dice, and the number of uncanceled hits during Neutralize Results would be the number of damage dice you roll. Damage dice would have basically equal chance of damage or no damage, and would mostly be unmoddable. Most current two dice primary ships would roll light damage, while everyone else would mostly roll medium dice. Certain weapons would roll heavy. Light would have 1 crit symbol, medium 2, and heavies Then you'd say that all primary attacks would roll two accuracy (3 at R1) dice, unless otherwise specified. That way you could have mods to change accuracy without generating way more average damage. Each extra accuracy die would generate an average of about half a damage, before you take into account green dice.
Plus then you could have torps and missiles fill different niches (missiles throw 3/4 accuracy dice, but only ever roll two damage dice on a hit, while torps throw 1/2, but throw 3 damage dice on a hit, as an example)