I was thinking about this problem last night. Fallout was released in 1997, Marathon finished the saga begun in 1993 that same year. Both are science fiction. Both are games for personal computers. Both are witty. Both are held as brilliant. Jess Heinig's NPCs in Fallout may have been equally as interesting as the AIs in Marathon.
Are they apples to oranges, too different to compare? Fallout was an intense roleplaying experience for me, and it was easy for me to identify with my character, but Marathon addresses the player directly as only a first person game can, guilt-trips and all.
Fallout brought its sci-fi savvy all the way down to the nitty-gritty of cell division, the FEV messing with anaphase to make a new molecule for genetic information; the difference between mitosis and meiosis is a plot point. Marathon, on the other hand, ignores certain probable limits on computing power (modelling and predicting every atom in a cloud?) to discuss free will, determinism, and even divinity.
They're both atmospheric, but they achieve different atmospheres in different ways.