Twenty Sided's Shamus Young took a moment to reflect back upon the two System Shock titles, while also pointing out some of the elements that he feels the classic FPS/RPG series did right and wrong.
For me the defining characteristics of System Shock were: Cyberpunk, RPG leveling, huge freeform non-linear gameworld, electronic soundtrack, pervasive solitude, and tightly controlled resource management.
The original System Shock has not aged well at all. The interface is grotesque by modern standards, and its eccentricities really detract from the experience. The story appealed to me on some deep personal level, but was it really all that great? Rogue AI gets loose, kills everyone. Lone survivor must fight the evil AI. It was certainly the right story at the right time. It constructed so as to not need dialog trees, or in-game cutscenes, or any of the other things games did poorly (if at all) in 1994. But the story itself isn't exactly radical. I've begun to suspect that the best parts of the plot were the bits I was filling in myself as I played.
System Shock 2 was far, far superior in terms of interface and gameplay, but the story suffered from a bad case of plot extension. The first game had wrapped things up and killed off the defining characters. The sequel tried to bring them back. It was a bit like how Fallout 3 kept waving old characters in our faces to establish its Fallout cred. The game dug up your nemesis, thus undoing your accomplishments in the first game. Then it let you kill her again. Then it undid your work again, leaving a cliffhanger that is never going to be resolved.