Woa, late to the discussion, so I will just give bullet point type things here.
- Plasma seige starships getting some sort of nerf to their shield penetration effect seems reasonable, though I don't think it should be a heavy nerf. Speaking of PSSs, did you say, Keith, that you would of reduced the engine damage it inflicted when you made it AOE and including fleet ships if you realized how high the engine damage was? Any chance of getting an engine damage nerf of ships hit by the AOE part?
- Armored forcefields getting partial resistance to PSS shield "splash penetration" seems like a reasonable buff, although I agree that there should be none that provide total immunity. Also, a bit of armor buff would be nice. EDIT: Also, they should be allowed to keep their ability to be armor boosted. This is one of the few ways that armor boosters can currently be actually useful on the defense.
- IMO, flak turrets are very nearly there in terms of finding a good spot balance wise. Their cap HP is already ridiculously high, so perhaps an increase in armor (== lightning turret armor seems about right) and maybe a slight increase to the number of things it can hit per shot, so it's effects can be a bit more visible before it likely eats some of the first damage of incoming enemies (especially if stationed around wormholes)