I think the factions are terrific, insofar as they have excellent reasons to exist in a grounded setting, are cohesive and consistent, and provide excellent motivations for any given character to support them or wish their destruction for ideological or practical reasons. I don't give a shit how empathetic they may be to a contemporary human when I can create myriad characters with varied points of view, see those points of view represented in game, and use them to drive my character's actions and story, differentiated from the journey of another character. What makes the factions seem imbecilic and inconsistent is their attitude towards the player avatar. Obsidian, and almost all RPG devs, are highly concerned with fellating their audience under the cover of "agency", such that said player character becomes the lynchpin to the setting, factional success, etc. The factions suddenly fumble, their ability to survive or propagate their influence always seems to rest entirely on one single operation, which is handed, with pleas and praise, to the player character. Probalby the only crpg I've played in which factions appropriately use the player is Age of Decadence, and even then, the power fantasy is redily visible and literal godhood easily attainable. I suppose other nominees include Pathologic and Disco Elysium, depending on the broadness of your rpg genre definition.
Yes, reddit will argue day and night over the most truly moral faction. I don't give a fuck about that. My character might be a pirate tweaker who takes slaves and blows shit up for fun and profit, or they might be a highly emotional trust the animancy valian, seeking to correct the savages and bringing the setting's equivalent of wokeness to the deadfire, or an utterly apathetic cold-blooded reptile of a cipher looking to make utilitarian connections in all factions. This is done well, and I'll shit in your pants if you disagree. Everyone will laugh.
The plot is a great way to drive the setting forward. An archipelago in chaos, with squabbling factions, is soil rich with opportunity for a newcomer and a good introduction for new players. The gods have their own intrigues, personalities, and ideologies to explore, lending depth and history behind surface-level conflict. That's all fine. But first of all, you're not really a newcomer, you're bogged down by some character history, because for some fucking reason they chose to make a direct sequel to two tonally disjointed games. So your character is fucked around with all this history that can have fun callbacks, but isn't really necessary and cramps your ability to play freely. Second, again, the gods must be personally involved with and, to at least some extent, respect the little baby turd of a player character, and the player take an active role in the mythopoeic plotline. This is entirely pointless, because it will proceed as required by the setting (which is good!) without player input. Might as well not have your main quest.