Jokes aside, is anyone else a little underwhelmed by the factions? As far as I remember, we have Rautai, Valian Republics, Pirates, and the Natives. For me, none of these factions stand out as particularly interesting. In contrast, New Vegas had House, NCR, Legion, Brotherhood of Steel, etc. Moreover, all of those factions were represented by rangers, BoS paladins, securitrons, etc. What do the PoE2 factions have? Sharkpeople and not-Italians?
The NCR and House have good and bad sides and presents an interesting choice. But with the Caesar's Legion settlements showing their good side cut from New Vegas, I never felt there were any proof in game that they were more than barbarian raiders and thus siding with them felt more like a generic evil choice than finding an interesting angle to justify the horrors they're committing. (I still love them though.) In Deadfire, this will hopefully not be a problem as none of the factions seems to be a conquering horde of slave troopers (the Pirates are ancestors of exiled princes and seem to be more like criminals with honor). So I hope we'll get more grey options than New Vegas when choosing which main faction to ally with.
As for your concerns, we know nothing of the factions yet. We don't know how the policies of the Rauatai and Vailian companies differ, what they're fighting over or what approach they're using to get it. We don't know if the Pirates eat people, or if the Natives throw outsiders down the rocks of Neketaka to appease their multiheaded cockgod. They cannot be interesting until we've learnt who they are, seen what their goals are, made us care, and then asked us to make a choice which faction to help and which faction to fuck over.
I had a hard time choosing between NCR and House. If Obsidian succeeds, I'll have a hard time choosing which faction to back in Deadfire.
I am not so much concerned about the faction's goals/motives (Sizzle did a good job detailing it) as I am with how the factions interact with game world. In PoE1, the factions were practically confined to one building each in Defiance Bay. At best, some had special weapons you could buy. In contrast, the NCR had outposts at strategic locations (with vendors), had unique weapons & armor tailored to their style, and further provided unique benefits (ranger armor, weapons, and I think a ranger could even be called in to aid you). Another example is the Brotherhood of Steel, who could set you up with power armor and weapons.
Beyond just morality or flavor, I would like to see each faction having a real presence in Deadfire with outposts and providing actual benefits (Rautai has unique armor and guns, Valian Republic gives money and animancy, Pirates gives special ship upgrades, local Sharkmen stay useless and reward you with sticks, etc).
edit: Deadfire reminds me of New Vegas to the extent that multiple factions are vying for a control over city/resource (Vegas/Hoover dam, and crack Adra/main PoE2 city). The difference is that we have not seen the same narrative or gameplay significance of the Deadfire factions, and PoE left me with a bad impression.