First link is a slightly different method of handling flux, Give it a spin and see what it's like, I can probably say it's not balanced but I can work down easier than working up.
I didn't play that long but I want to write down my opinions so far.
So from what I understand (correct me if I'm wrong), you greatly increased the flux capacity and greatly decreased the flux dissipation rate for most ships, which reversed the Neutrino's uniqueness in handling flux into the opposite method. The shield efficiency was also lowered to 1.0. This maintains the Neutrino's endurance in face-to-face combat, but once they hit their limit in flux, they are sitting ducks, especially because they are slow and it takes so long to vent the enormous amount of flux.
I think this definitely makes the Neutrino weaker, especially in prolonged combat because eventually flux vent would outweigh flux cap. Because of this, they become much more susceptible to hit and run strategies. It should also put a strain on Neutrino ships on always going for crazy dps weapons instead of flux-efficient weapons.
But I'm personally against this idea because it seems to make gameplay bland. Because Neutrino are often slow and have low maneuvarability, it's hard for them to strategically use this way of handling flux. Most of the time, I found myself trying to close in and throw all I've got before I hit high flux or the enemy escaped. If the enemy was enduring, I'd just fire everything-vent-fire everything-vent until the fight was over. Currently, I think this is the best strategy to fight regardless of the situation, since fleeing and venting in between is not feasible due to slow speeds.
On the side of the opponent, I didn't feel a need to go around the shields as I did before, because it was easier for me to kill off Neutrino ships after they hit max flux and were vulnerable rather than to try to kill them faster when they could still hurl weapons at me (similar to fighting an onslaught or conquest).
On the other hand, before I had to be careful with handling flux because of the low flux capacity (although this became trivial with larger ships that had useful flux caps). If I fired high flux weapons too much while fighting, I could instantly hit max flux and become overloaded. This is why I thought Neutrino frigates weren't that strong because despite their high shield efficiency, they overloaded very quickly with ship-system and weapon usage while they also lacked the speed advantage of other frigates. Coupled with the small shields, I had to be cautious of when to dive in and pick a fight and when to silence weapons and vent flux.
I personally think the original method in handling flux (high vent, low cap) was better because it requires strategy to use effectively. I also think it's unique since I don't know any other faction that uses high vent, low cap like Neutrino does. But I guess it would be harder to balance since most of the time, high vent=high fire power and defense...
Anyway, What do you think about lowering the flux capacity for larger ships even more, like halving? That would put an op strain on weapons and burst flux usage considerations, and also increase the chance of overload, which are most of the weaknesses of Neutrino frigates.
