Bioshock. Yeah, the two System Shocks came first, had deeper gameplay, and took everyone by surprise with one of the greatest plot twists of all time. But I'd argue that the overarching plot of Bioshock--along with its environment, history and characters--is better developed. It's chock full of literary and sociopolitical allegory, and.. ..while its own plot twist is less original than that of its spiritual predecessors, Bioshock actually poses some interesting questions about the nature of morality and control as they pertain to video games; the various brutalities and atrocities committed by Jack could have been attributed to Fontaine's mind control... Except that it is ultimately the player themselves who has opted to guide Jack on his murderous, harvesting rampage through Rapture.
Silent Hill 2. Tremendous atmosphere, deliberate pacing, characters with alarming but well-realized motivations, a tendency to constantly manipulate the player's emotions, and a genuinely powerful resolution. Despite some occasionally stilted dialogue and voice acting, Silent Hill 2's story shines through as one of the most mature and tragic ever told in a video game. And it is relayed to us from the perspective of what might be gaming's greatest unreliable narrator.
And to complete my triptych of apparent unoriginality, both Mass Effect games. The story as a whole is actually kind of bland; recruit team, save universe from unspeakable evil, repeat. But the detail put into the game world is tremendous, from the technology to the politics to the motives of the characters around you. The characterization and dialogue are superb, and the ability to choose the protagonist's conversational tone is a great example of an edge video games have over other narrative mediums. The plot is a cliche, but an intelligently written, finely polished, uniquely approached cliche.