I often wonder if John was involved with the story telling aspect of his games, not just the code.
That's not to say he didn't have influence; many times the games' stories were derived FROM the tech, not the other way around. Doom was originally supposed to be much more story- and character-driven, but that took a backseat given the focus on the development side was on the gameplay mechanics.
Also, this quote:
> Story in a game is like a story in a porn movie. It's expected to be there, but it's not that important
From "Masters of Doom".