Having read none of the lore regarding anything to do with any game ever, let alone Elite. I would love it if the 'Thargoids' were hostile from the beginning, for whatever reason. Kind of like Freespace.
And they should be almost invincible, and use technology that's completely different and vastly superior to ours.
They also should get a new name cos 'Thargoids' just sounds like a nasty disease you've picked up. Lol
Most of the CGs should become war oriented, the first could be recon and gather intelligence to find the next attack, then fight off a certain number to prevent the fall of a system. Then you have salvage of Thargoid ship wrecks for research. Finally would be counter attacks on Thargoid systems.
Also we would need an AI overhaul cos 100s of Thargoids doing kebab rolls would not be threatening. Lol
They should get their own distinct AI. So they fight and fly like nothing we're used too. Swarm logic or hive oriented would be good. But with a hierarchy still, and still lethal when alone, but weakend.
Fighters slaved to Conda sized ships, which in turn are slaved or capital sized ships and so on. Maybe have the ability to shield share when in groups.
TL

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They need to feel Alien, and be extremely deadly and relentless, and like nothing we're used too. Or its just gonna be CZs with different ships.
And for a rough idea of how strong a single Conda sized ship should be?
5000+mj shields. All huge hardoints (at least 8). Turrets and missiles that can't be spoofed by current counter measures (CG for research!), And initially, you can't target subsystems cos you have no idea where they are or how anything works, until you've researched enough salvage.