So, the way we deal with minor factions is that we assimilate them into our empire, either through peaceful means or by force. This is heavily incentivized, as it makes them stop producing roaming pirate fleets and your empire also gains their affinity, which is pretty nifty. However, this poses problems in a couple of ways, primarily for the Vodyani from what I have seen.

Firstly, the Vodyani don't assimilate them like normal, instead converting them to their religion Cultist style. But, unlike when another empire assimilates, the minor faction remains there, and can be converted by another Vodyani faction, as I've had that happen to me, and I suspect they can be assimilated by a non-Vodyani faction as well. In addition, I was hoping that when converted a minor faction would function as a permanent food source for te Vodyani, but I was unable to use them for Essence. I don't know if this is intentional or a bug.

Second, since when a minor faction is assimilated, it doesnt remain afterwards. As the Vodyani I was on my second quest, to convert a minor faction, but 3 times I neared conversion only to have the sophons assimilate them right from under me. I of course exterminated the Sophons from the stars, but after conquering the sophon systems, it auto removes all population, including the minor faction, and they don't remain for conversion or assimilation. This aspect seems to put the Vodyani at a disadvantage when it comes to minor faction manipulation, and it also left me unable to continue my main quest line as all other minors had been assiilated, which seems like a huge problem for a major faction to have.

I didn't see anyone else talking about this so figured I'd start it off.