I don't think Neutrinos need a buff, they are already the top dogs in the sector, including other vanilla balanced mods.
I played a bit with them on 0.6. I expected them to have much more punishing CR reduction. Frigates got a 5% CR reduction per deployment, 3 times less than a hound! And without CR deterioration per second on top of that. Destroyers and Cruisers are more reasonable but capitals ships are still extremely easy to deploy which seems weird to me. The Unsung cost 15% CR, such a gigantic high tech monstrosity should require a lot more efforts to ready for battle i think. Same apply for other big ships.
The supply daily cost is reasonable though, high techs ships need to be supply hungry! However i was still surprised about the 3 daily supply for the Polarity freighter, that's a lot for such tiny ship who can't even defend itself in combat even though it's pretty handy (and dirt cheap) for additional cargo space.
Otherwise i like that Neutrino can't install the extended shield hull mod. Their tiny shields are their best strength as well as their worst weakness. However i agree that it is difficult to use such a tiny shield for the player, especially when you are getting showered with Annihilators. The AI don't seems to have that problem, and with a wider shield arc, that would be overpowered. So yeah, i like the Neutrino sigma upgrade replacement for extended shield.
Other than this... I found something weird with the Causality frigate. It got the built in phase missiles as well as the phase missile ship system. That's a bit too much i think, could replace the ship system with something else (flares maybe? the Causality is already very powerful, so avoid adding a system too strong.) Oh and also, you should put the phase missile on auto-fire on the variant. Without it, it won't launch its missiles against frigates.
Speaking of phase ships. I have yet to fight a Causality and a TheEND but i know they have the ability to stay permanently phased, which can cause some problems for the player. If it want to retreat, there is nothing i can do to prevent him to do so, he can just wander around the map without any risks. Worst, what if it don't retreat, but still stay phased the whole time just to troll the player, waiting him to give up and retreat? I wouldn't surprised it would do that kind of trick, it already do something quite similar by engaging without any ships to deplete the player CR. You should try to add a theEND in a fleet to see how it fare against the player (i'm not sure the Neutrinos AI are actually using phase ships in fleets).
The Unsung, as other have said before, is still op as hell. An Elite variant piloted by the AI managed to take down alone the whole Hegemony SDF. The problem of the Unsung is, i think, it have too many weapons mounts. The six large universals are fine, after all it is supposed to be a powerhouse. But i think it got too much rear guns. The only way to take on a Neutrino ship is to avoid the shield, which is usually facing the front, but in the case of the Unsung, even the rear is capable of taking down capital ships. The HERP emitter is pretty crazy as well, you can one hit kill everything in the game (save the Paragon with its shield).
And as someone said it before, the Drache bomber seems bugged. It can deliver its bomb but can't resupply for a second run.
Aside from this, i think everything seems pretty balanced. Ah i forgot, the Falken is pure lolz in the campaign.