In retrospective, Neutrino is probably in it's weakest state in it's existence as it only has received nerfs, with a sole exception of the jackhammer since the remodeled hull actually allows the ai to utilize it's main weaponry.
These ships aren't just powerful. They're clearly overpowered. Nearly every ship has it's own superweapons, combined with almost unbeatable shields and ridiculous flux dissipation.
I currently am running a game as the BlackRock faction, and I have some seriously powerful ships, that can whoop ass on most things. Yet when I toss even the FRIGATE sized ships of the Neutrino faction against my CAPITAL ships, they still put up a serious fight. The capital ships are in a whole different league. Even with a ship with 12 torpedoes, 2 Cains, and 2 Twin-barreled Railguns, as well as other KINETIC weaponry, it still takes everything I have to force their shields down at all, and I almost NEVER cause them to overload.
Those MIRV launchers that launch the Red glowing missiles that magically turn into 30 projectiles are way overpowered as well...allowing even tiny ships equipped with them to overwhelm even Dual Thunderstorm defences.
TLDR: Balance this please. We all understand how COOL it makes you feel to make a faction that can kick everything else's ass, but it really doesn't make for fun gameplay.
I'll say it like this, If you're using your capital ship to fight a neutrino capital ship, you'll lose 7 times out of 10 unless you have some massive range/ kiting ability.
The best method to beat them is to not be in a situation that is trading blow for blow.
Maneuverability is your best defence against the (Anti-Capital) firepower most Neutrino capitals use.
Swarms of smaller ships (or fighters/bombers those do pretty good) will beat out the defences.
Use a mirv launcher and you'll do a serious number on probably 80% of neutrino ships as the arc can't block all of the missiles.
I've already labelled it as overpowered so I'll only change them as I see fit

If you feel like making them weak, just change the Shield effiency to 0.6-1.0 Good Luck!