Oh, ehehe, th-thanks HELMUT.
Uh, anyway, glad you like the faction; the more I've worked on them the more thought I put into the role of each ship and how they fit together (at least in theory) and I'm glad to hear that they're each as different from each other as I'd hoped.
Anyway, on to the specific points: The Seski indeed was actually started as kind of a Hound analogue, though not nearly so good a freighter, and due to her general frailty she's a pretty different ship in terms of usage; I've never actually been terribly good with the Seski, though.
The Sargasso is indeed supposed to provide a benefit to fighters while its system is up, making them somewhat more maneuverable (+100 acceleration, 50 deceleration, 150 turn acceleration and 100 turn speed) and give them a slight boost to range and accuracy. It also boosted speed during the earliest phases of the testing and if memory serves that was being applied correctly, so I believe that it's applying the maneuvering bonuses as well, though it's kinda hard to tell.
Also, with the way the script is set up, if the bonuses are getting applied multiple times, well, that'd be a bug. I still need to come up with an animation for this though, to give a visual cue that it's working.
The Tartarus and Scylla are both pretty monstrous. Actually given the Tartarus' siege mode and it's general effectiveness I suspect that her Deployments costs may need to rise a bit. As for the Phased Graviton Beam, it is indeed a slightly better Graviton Beam, in that it has a bit of emp damage; there been some suggestion to reduce it's range so that the AI doesn't linger outside of other weapons ranges.
The Pandora Array is the trickiest thing to balance, and I've definitely had to tweak something or another about the crazy thing way more commonly than any other aspect of the mod. Still, I kinda like it being a bit risky to use. Regardless I'll take a look into tweaking it some more and see if I can't make the thing slightly more reasonable. And I still need to set up a custom AI for the Elysiums combat routines so the AI can at least keep the weapon pointed downrange while it's charging it to fire.
And yeah, having a heft CR cost, well, like Alex noted it's another way to balance ships that could be overpowered so that they become more reasonable. On the Morningstars CR cost, I was generally comparing it to the Medusa. Well, maybe not the best thing to compare a player controlled Morningstars effectiveness versus an AI ruled Meddie. I guess I'll do some adjusting.
The Lambent 0% deployment cost thing is a bug in Starsector with automated craft; having no crew means they can never recover CR.
And for the last two notes, yes, and yes.