Especially American writers - everything is happening in allegory for modern day America, still remember the moment I stopped playing Pillars of Eternity 2: one of NPCs, fisherman from carribean-like village, started ranting about horrors of colonization, but from the position of progressive college freshman.
Funnily enough, I have the exact opposite complaint as you about how Pillars of Eternity II handled colonialism:
The fisherman was, from what I recall, trying to get his land back after his village was effectively made to sign a predatory deal with a colonial company backed by a large state: Perhaps you may take issue with the exact way and nuance of how the fisherman said it, but right there that's establishing an interesting theme of colonialism.
Whenever I think of how POE II handled colonialism, I think of MrBTongue's video on discomfort, where he argues the point that a lot of video games try and give the veneer of moral ambiguity, but stop right before the point it becomes uncomfortable, because too much moral ambiguity would make the player hesitate, whereas embracing the uncomfort is a positive
A big part of the issue I take with POE II's writing, is it doesn't portray
enough of an anti-colonialist struggle, nor enough of colonialism as a system of power, which makes it feel kinda just hollow and tacked on. I feel a large part of the reason for this is that Obsidian figured "We need to make this game morally grey and with different factions all with their own flaws, therefore we can't go overboard"
Real world history is incredibly brutal, but Pillars of Eternity 2 feels like it's toning down the brutality of systems of power in order to make it seem more morally grey and like all of the factions have a point. How I would have written it would have been more among the lines of
1. Make slavery an active persistent problem in the Valian Republics that's an issue throughout all their colonies, rather than an underground illegal business practice. Don't make it all doom and gloom, I'm sure there are some Valian Abolitionists, but the horrors of slavery come from precisely the fact that it was a completely normalised and above ground, so making it as this shady side business the Valians are engaging in kinda makes it lose some of it's bite.
2. Actually take measures to emphasise violent occupation. Like ok so part of the factional conflict is that the Valians are they're a trading company that's exploiting local for profits, as opposed to Rauatai which has a burgeoning nationalism, which wants to violently unify the Aumau people in to a singular nation state. This is incredibly interesting on a surface level, but the problem is they're not willing to fully emphasise the violence that the worldviews these people have will inevitably involve
Like, this could be fairly easy: Show far more of the actual conquest that Rauatai is engaged in, and make it an active choice to help them conquer nearby tribes. In the case of the Valians, have them get you to protect their property from the violence of locals, only to find out the land their property is on was taken from the locals in some dodgy exploitative trading agreement.
3. Have the Huana seem more genuinely resentful. They should feel like a culture that's trying to avenge a massive cultural trauma gained from their loss of sovereignity to foreign occupation, not just weird traditionalists.
4. Have the pirate ending seem far more like a fragile social order, like it could potentially collapse if any of the major factions made a move.
There's already in my mind, plenty of interesting questions that could be asked in POE2. The Valian Republics are on the verge of a scientific revolution with a new type of technology, Rauatai looks like a potential Industrial Powerhouse, held back only by it's seasonal storms stopping it from creating the agricultural base necessary for full industrialisation.
The game could ask you "Do you think it's the right way forwards to choose one of these potential futures, either the technologies that come from Industrialisation, or from the unique Animancy Soul Machines that this universe have, and thus choose a potential progress for this universe, if the cost is having to enable violent systems of power". It would ask questions of how much the player values technological progress and industrialisation, over the self-determination and national sovereignty of peoples, and whether they think violent occupation is acceptable as a means to an end. On the other end it could ask how far colonised people can go in trying to overthrow their oppressors: What happens to all the Valians and Rauataians who live in the Deadfire after the systems protecting them break down?
And it would feel like it would have genuine moral weight, since the game wouldn't be playing around with how brutal all the major players involved are.
Instead we have a game where all the factions feel vaguely friendly with a few minor flaws. This doesn't feel like having to choose out of a series of different violent systems of power, ones where their values don't necessarily align with your own, and thus question in the process where your values lie. It feels like choosing between a series of equally moraly grey endings because they haven't really thought about how to make the questions being asked have any actual weight.