This is just an idea ofc, and while it would be awesome to be implemented and created it’s really just me wanting to express my ideas 
Sooo, instead of being a flat 2D game it would become 3D, Homeworld style battles but with minimal ship control. The third dimension would ensure even more tactical ship placement and have reason for those missiles to over or undershoot ships (-.-). When designing ships you would be given an even more basic chassis, and have to equip wings (with hard and standard points on them obviously), and thrusters aswell as the engines to fuel them (thrusters would be an even more important part in ship building now, as they would be far more expensive, have an aesthetical look to them, and be thus feature an important part in the ship building process, as a good thruster would mean less guns (:(). Thrusters would have their own module slots). Armour would be more solid, and would require blasting away (and would be applied in sections, so say this is the ship
. <[-/
<=o==========:===]>
. <[-\
each colour would be different armour sections, and an armour module would hold a “Coverage Space” aswell as “Resistance”, “Damage Absorbed” and in battle there would be an “Armour Overlay” which would show you the percentage of armour of each section of each ship.
Weapon placement would have an affect on its targeting radius, (as it is now 3D, remember), and for obvious reasons a beam laser placed on the bottom of a ship couldn’t shoot an enemy flying above them.
You would be able to, in the deployment stage, be able to order ships to attack individual enemy ships, rather than just telling them “Kill so and so class ship more than other class ship from this range”. This ship would be the target priority until it is destroyed, and the ship would then be free to target its secondary priority ships (you can specifically target more than one ship), until all targets specified are destroyed and THEN, it will target whatever ship it pleases as set by the sliders of GSB.
Damage to ships would be much more visible and not set by a picture. You would sadly have to develop ships in two-three layers in 3D programs such as 3DSMax and the like, which would alas, make it harder for modders (but so much more satisfying to see a large section of ship be lasered across the ways by a well placed laser shot). Hulls would split into random ragged chunks after ship destruction.
I will add to this later, and I hope for now you enjoy my suggestions (And maybe even Cliffski will see it :D)