With regards to The Witcher 1, I feel compelled to defend its quality as a story, even though I prefer The Witcher 2. Despite me thinking that the latter was in general superior or more fulfilling to my tastes, the first game was still very good and complex, especially if we look at the 3 primary components of the main plot.
1. The Order vs Scoia'Tael plot is one of the few representations of a gradual escalation of violence and extremism that I think was done well. Both sides are presented with nuance, and we see both become more and more extreme in their actions, as violence slowly escalates into what eventually turns into a full scale rebellion. It is very difficult to properly convey the phase of escalation, especially when it comes to internal revolts, with as much nuance, focusing on many different factors, and as much patience. Yaevinn especially remains one of the most interesting (and certainly very flawed) characters in the series imo.
2. The Identity Quest. This is not Planescape Torment level, evidently. But that iconic (and unrivaled) example aside, I've not experienced an RPG that makes such a big and explicit emphasis to your character actually establishing an identity after amnesia. Even better, the game actually reacts and acknowledges your choices and lines of reasoning, and doesn't just let you RP fully in your head like what most RPGs do with few exceptions. Every choice became part of this quest for identity, making the gravity of choice not only external, but deeply internal as well. That to me is rare.
3. Jacques de Aldersberg. It is true that on paper, Jacques may appear to be a generic villain, but that would be a superficial reading. In many ways, he is a product of your own choices and reasoning, and the game explicitly appreciates that by having him use and twist arguments that you yourself have used when he was a child. Jacques is a deeply tragic and disturbed character, and while his plans may be generic, his character is not. In another story, he would have been the hero (much like Ciri). But instead the game gave us a man crushed by the weight of his own messiah complex, mentally damaged by constant visions of apocalypse, obsessed with salvation.
The Witcher 1 had a lot of flaws, but I think its story was excellent and surprisingly well presented.