I kinda feel like the different factions aren't quite as unbalanced as some people are making them out to be, people seem to be looking at a faction or weapon's strength while ignoring its weaknesses.
The Neutrinos might be good at auto-battle, but auto-battle doesn't affect the player very much, and their shields leave a rather large portion of their ships exposed, leaving them balanced in a regular fight.
The Antediluvians might have a huge amount of armor and firepower, but other than their burn drives which leave them unable to turn, their ships are kinda slow, unshielded, and their weapons have a very short range.
The thule meanwhile have especially good weapons on their ships for the ship size, but they have no shields and only average armor, leaving them vulnerable to anything that out-numbers them.
The blackrock ships may have more than the average number of weapons on their ships, but their weapons are almost all short-ranged and for the most part balanced.
As for the IF's more powerful weaponry, I feel that the only thing that might need a small nerf is the hadron accelerator. I kinda feel that their other weapons, while powerful, are balanced by their large flux cost, large ordinance cost, and large cooldown to fire. Vilu was able to make a pretty powerful ship based off of a few of these guns, but he did so by stripping every other weapon off of the ship, and isn't the point of the refit screen to make a more powerful ship anyways?
As for the junk pirate capital ships, I've also noticed the problem. It seems like the crew requirement/capacity levels might need a tweak.