Re: Your Favorite Video Game, Story-Wise (and why)
Planescape: Torment, and most anything by that team and its descendant companies. I mean Alpha Protocol was not a well-assembled package, but had an insane amount of research behind the humint aspect.
Spec Ops: The Line. Players revolted against a plot that failed to give them feel-good cookies for bombing people, which I think was a great precursor to the emotional complexity behind GamerGate.
Star Control 2. Video game humor is often still the most idiotic thing imaginable, and attempts to blend serious and silly tend to fail spectacularly. SC2 had some of the most sophisticated writing imaginable for a sequel to a basic head-to-head combat game. Giving whole backstories to simple sci-fi tropes and then making them come alive in a whole tapestry was one of the more incredible, unsung feats in game writing.