( Reposting while adding further thoughts and additions in an attempt to shine some light on how this would work.)
Battleship: Ion tech to level 15 multiple ion shield generators are implemented 20% shield boost. Laser tech to 20 Laser cannons are retrofitted causing a 10% weapon increase.
Battle cruiser: After plasma tech level 12 the battle cruiser is retrofitted with plasma cannons and plasma shield generators, causing a 20% bonus to shields and damage. (It is not affected by the 5% gain of plasma every level)
Destroyer: After plasma tech level 15 Retrofitted with plasma shock wave cannons, allowing 5% bonus to damage. After zorg physics reach's level 5, a better understanding of the destroyer's engines allows them to go 10% faster.
Before After
Battleship: Weapons 1,000. Shields 200 Battleship: Weapons 1,100. Shields 240
Battle cruiser: Weapons 700. Shields 400 Battle cruiser: Weapons 840. Shields 480
Destroyer: Weapons 2,000. Shields 500 Speed 5.000 Destroyer: Weapons 2,100. Shields 500 Speed 5,500
All upgrades occur after WSA, and are not scaled, meaning that if your weapons are being boosted by 140% on the battle cruiser, the boost will still only be 140 on the weapons, not changing to WSA.
Part Two.
Upon reaching level 12 impulse, a better understanding of how space travel works on smaller craft is founded. Impulse jump drives are fit as replacements on light fighters increasing it's speed from 12.500 to 15.000 and causing it to adjust to impulse engine.
Upon reaching zorg physics 5, and plasma 10, a new development is reached, allowing for the fire power of plasma being compacted into smaller cannons to be attached onto the light fighter. This allows for it to deal more damage, but due to it being compressed in size, it does not benefit from the 5% boost per plasma level. Attack points before: 50 upgraded to 75-90(Still needing tweaks and further consideration)
(This one is just for laughs but perhaps it will take off.) Upon reaching hyper space 13, a new method of engine reformation is tested and approved for retrofit. The engine is moved and attached onto the colony ship, allowing it faster movement at the cost of increased deuterium consumption. Base speed upped from 2.500 to 3.250. Fuel consumption is upped from 1.000 to 2.500.
(I know there is going to be at least some feed back negatively towards these idea's, and will need a lot of input on this, as I am not sure how smart it would be as it would completely kill combustion engine if all other advancements where implemented.)
Reaching level 15 impulse engines become exceedingly advances, making other engines meek in comparison. After careful consideration, trial and error, the impulse engine is re-sized and refueled to work on the recycler. It is considered an option upgrade for those willing, but once picked it may not be revereted. The recycler gains considerable speed, but also gains considerable deuterium consumption. Base speed upped from 2.000 to 3.000. Fuel consumption upped from 300 to 480. (This idea is to think that the bigger players can get it faster but at a much more expensive cost.
Actions necessary would be tying a new system into the weapons development similar to how the engines currently work now for the small cargo, when improved into impulse already. Same for the engines, if possible extend and edit for the new values, tweaked before implemented and such. This is giving that I am not adding any sort of new research, building, or ship required to add these upgrades. I thought I'd keep it simple so the developers don't cringe
Thoughts, comments, feedback extremely appreciated. Will do further tweaks and math as I rethink fairness with cost.