There are like 5 games ever that are morally complex. Most games that let you choose between two sides let you pick between a faction of fascists or ineffective cultish hippies. It's rare for games to present better ideology than those.
Off the top of my head, I can only think of a handful. Disco Elysium, Fallout: New Vegas, Planescape: Torment, Frostpunk, Caves of Qud, Vampire TMB. All of those have writing that allows the player to explore what good or bad are in the right situations. DE is probably the best I've ever seen in a game, an absolute masterpiece that shows you the consequences of the bad moral choices, and yet also explores why you might choose the good ones.
I haven't played Baldur's Gate 3 yet but I'm told the writing is actually pretty good, so I'll check that out.
I would say there's a definite theme of refugees being scapegoated by bigots and xenophobes, and those bigots and xenophobes falling into evil. Kagha, Bahl cultists, the people of Baldur's Gate, etc. are all blaming everything on the tiefling refugees. There's a definite positive theme of inclusiveness and not being close-minded
I got a little sad when my character told a bigot to shut up, he told me some bs, and I called him out for being foreign too. (one of the better options given)
I then blow him up with a fireball after the crowd agrees with me and turns on him. Of course, the game sees it as murder, because they didn't code it to be different, but damn in my canon that guy is a pile of soot. It kinda sucks that only RPGs like BG3 are brave enough to take the stance of "Remove all bigots by force if needed", but only because killing Evil McMurderlord is fun. But I'm glad at least they let you say it.
Yeah, that's what I mean, it's basically the same morality as a Dragon Age or a Mass Effect. "Mean people and racists are evil". Which like, they are, but it's not particularly deep.
Morrowind as well, all the factions suck (except the anti slavers), and hate each other, but complex material systems of oppression and co dependence trap them in a decaying structure and have caused even the more noble institutions to be corrupted. And now that system is no longer capable of defending itself.
You may or may not be the Nerevarine, and even if you are it's unclear what that actually means and if it's prophecy or you taking it "by violence". But you can use the fact other people think you are to break the cycle.
Of course once you have there's no guarantee of anything better on the other side, you're just some guy, you know.
Some of the Shin Megami Tensei games are really interesting in that regard, because even as they portray the ideologies in their super-dogmatic form and in some cases as everyone-sucks (including the status quo supporters), games like Devil Survivor 1 or Strange Journey actually have writing so good that they make choosing sides not obvious and feel like they actually have weight on the future of humanity in-universe.
Others either flop on their face (SMT IV), or have very clear biases (SMT I or II)
But hey,
SMT II
choosing the Chaos ending, allying with Lucifer and the Demons of the Abyss to destroy the Abrahamic God's flying Noah's Ark, to free the world's oppressed and left-to-their-own-misery subclasses from a theocratic, hierarchical dictatorship... leading to a world where both the mutated humans left on the surface after 1's events and the demons could co-exist in relative harmony - all while rejecting the title of the Messiah.
...is a great ending and it doesn't matter if the other two don't compare.
(I fucking love this game, I eagerly await the day when the translation of the PS1 port comes out)
Since BG3 exists within the lore of Forgotten Realms, evil isn't nearly as complex as, say, Disco Elysium.
Like sure siding with the slavers is easier than siding with the slaves or X Y Z amoral choice may give you an otherwise unobtainable reward for doing strictly the good thing, but it's not that deep.