Huge BSG fan who knows way too much about the show and its lore, I just couldn't resist writing this ridiculously long list of suggestions and recommendations for this great mod you've created! Please take my numerous suggestions as evidence of how excited your mod made me; I hope all my unsolicited advice doesn't feel like interference :)

(As an aside, I have some experience with Photoshop and will see if I can make the studio photos of the humanoid Cylons look more appropriate for Stellaris---I agree that constantly cycling the humanoid models as leaders would be really cool!)

TRAITS: Strong, Natural Engineers, Rapid Breeders, Repugnant

I removed "Resilient" not because it's off-theme, but because I find it to be a fairly "meh" trait, excitement-wise. As for "Venerable", I removed it because it does the opposite of what (I think) you intend (i.e. to represent the Cylons' immortality), by drawing attention to Cylon life spans (and making it even more clear that we can't get immortality for our Cylons in Stellaris). I think it's better to take this theme out of the traits entirely, and instead insist that "death" is really just a return to the Resurrection Ship, and the "replacement" leader is really the same Cylon.

Adding "Natural Engineers" is a no-brainer: the Cylons should be experts in robotics-related technologies. "Rapid Breeders" simulates how easy it is to copy and mass-produce Cylons--as long as we pretend those "Food" tiles on planets are actually "Silicon Deposits" or whatever :)

ETHICS: Collectivist, Militarist, Spiritualist

I think Spiritualist is really important to include, as the Cylon's monotheistic religion played a huge role in defining their motives and story arc, and was ultimately what caused them to fracture towards the end of the series.

As for what to remove, I wouldn't count the Cylons as "Fanatic Militarists" at all: Only Cavil fits that bill. The rest either stayed with him out of convenience/apathy, or quickly concluded that destroying the Twelve Colonies was a mistake and ultimately rebelled. Sure, the Cylons did wipe out the Twelve Colonies, but the fundamental nature of a species shouldn't be decided by a single event---the entire series was merely a single short war told from the losers' perspective.

GOVERNMENT TYPE: Military Junta

A "council of high-ranking military officers who oversee all matters of state" is a better description of the joint leadership of the seven Cylon models, than an absolute dictatorship is. The seven Cylon models voted on matters of war, and often disagreed; they didn't speak with one voice. The title "Archon" also sounds more Cylon than "Grand Marshal", methinks :D

STARTING WORLD NAME: "The Colony" (or "Caprica")
STARTING WORLD TYPE: Tomb World (or Continental)

The Cylon homeworld is and always was "The Colony"---from the end of the First Cylon War fifty years before the show started, all the way to the series finale (when Galactica blew it up). If the name "The Colony" doesn't work with Stellaris' naming schemes, than I'd suggest "Caprica" instead. But it's definitely not Kobol; the Cylons barely set foot on Kobol.

As for World Type, I know a mod has made "Tomb World" a valid world preference... I wonder if that would work? Otherwise, I agree with Continental---it makes the seizure of Caprica make sense. (Caprica could also be a Tomb World, though, after the holocaust.)

FLAG: Two hollow silver pentagons, one inside the other, on a field of black.

The Cylon logo is two pentagons, as seen here on the raider's wing[www.cybermodeler.com]. It's the symbol of the corporation where the first Cylon was built, and I think it feels more "realistic" as a logo the Cylons would choose compared to an angry Cylon face.

I think a silver one of those on a pure black background (or maybe a tessalated hexagon pattern like this one[orig06.deviantart.net], with black and a dark grey or even purple as the two colors) would be perfectly Cylon---very machine-minimalist, and rather ominous.

Again, sorry if I came off as pushy or overly critical, I really love what you've done with the mod so far!