3000*4 hp fighters vs similar but 300 hp for vanilla is a bit overkill.
They have 1750 hp, not 3000. That's a big difference. That's a total of 7000 in a wing, not 12000. The Persephones also have weaknesses which have already been discussed. Back then I also said that I may tone down the ships if they prove too unbalanced. It should be noted that they are not nearly as strong as a frigate, as they only have 1750 hp and far less armour.
There is no balance, some factions are more powerfull then others
There's balance. Some factions have their own strengths and weaknesses. Perhaps you're still to discover them.
aqvidulians - (sonic guns for space usage and water lasers...) completely idiotic ship size to durability ratio, 3000 * 4 figher wings with size of wasp that extremely hard to hit by hand and capitals with burndrive and 40 mounts, not really fun both to play with and to farm em.
with proper strategy completely unkillable.
Sonic guns for space usage and water lasers? What about them? It is no more far-fetched than mass drivers in space. Or plasma guns and laser beams. The Sonic Turrets create a powerful fibration within a cilinder called a drumchamber. This is done in an area of the ship that has gravity and molecules to manipulate. When the fibration is powerful enough, it releases a destructive pulse that continues outward into space. Much like a mass driver may ignite an explosion that generates enough energy to send out a solid object into space.
The Reflector Turret uses a series of tiny lenses that contain water, called aquapools. Light is being shot through the lenses, through which the beam picks up power untill it is capable of cutting through solid objects.
Antediluvian ships have many mounts, but only low grade weapons. The burndrive is part of Antediluvian tactics and survival, since their weapons are short range and they do not have shields.
neutrino - 0.16 shields and 2-3 times more HP\armor then same class vanilla ships, kings of autoresolve, never saw neutrino fleet losing battle. Still can lose to figher swarms.
More powerful shields may make Neutrino ships too powerful. They already seem to have high hull and armour ratings. I agree that they seem to always win autoresolve situations. That might have to be looked at.
blacks, thule - basically all ships have firepower of next tier, eg frigate have firepower of destroyer, in other terms stay on same level with vanilla.
They have powerful weapons, but terrible speed and other weaknesses. They seem balanced enough. As long as their fleetpoints and cost reflect their power, it doesn't matter what classification (frigate, destroyer, etc.) they have.
I'm just going to drop my little tid bit in.
The placement of planets and stations should be looked at, early in the game some factons have absurd levels of dominance, and even into late game resupply fleets have a nigh impossible team getting to their destination, EXCEPT for the factions whom have planets on the outer reaches of the map.
Also, your logic behind the Antediluvian weaponry isn't quite on point. Water presents no benefit to laser weaponry, infact in the way you've explained it it seems to make them completely useless.
Also, Sound requires a medium to travel, there is no medium in space for sound to travel through so sonic weaponry makes no sense whatsoever.
Instead of trying to explain it you should probably just say. It's magical! I ain't gotta explain ***!
A Persephone fleet with maybe two carriers on the fridges of a battle space seem to be capable of infinite regeneration so long as one fighter makes it away, which would be the case because currently you require a dedicated barrage of multiple medium class weapons to kill them. Despite their supposed low armor.