The Powerslave and PID comparison I did before doesn't have nearly as many similarities to that of System Shock and Marathon & PID. The latter actually has way more than I thought they'd have. Listed is a series of talkthroughs of the two System Shock games (at time of writing them) with a total list of how they compare to Marathon and PID at the end.
These talkthrough bits like the Powerslave one are important as it's easier to detect any similarities as I describe the game, especially when it comes to listing them all at the end, plus some people might spot ones that I didn't.
System Shock 1
Episode 0: https://forums.bungie.org/story/?read=75018
Episode 1: https://forums.bungie.org/story/?read=75019
Episode 2: https://forums.bungie.org/story/?read=75020
Episode 3: https://forums.bungie.org/story/?read=75021
Episode 4: https://forums.bungie.org/story/?read=75022
Episode 5: https://forums.bungie.org/story/?read=75023
Episode 6 (FINAL): https://forums.bungie.org/story/?read=75024
System Shock 2
Epsisode 0: https://forums.bungie.org/story/?read=75026
Episode 1A: https://forums.bungie.org/story/?read=75027
Episode 1B: https://forums.bungie.org/story/?read=75028
Episode 2: https://forums.bungie.org/story/?read=75029
Episode 3: https://forums.bungie.org/story/?read=75030
Episode 4: https://forums.bungie.org/story/?read=75031
Episode 5: https://forums.bungie.org/story/?read=75032
Episode 6: https://forums.bungie.org/story/?read=75033
Episode 7: https://forums.bungie.org/story/?read=75034
Episode 8: https://forums.bungie.org/story/?read=75035
Episode 9 (FINAL): https://forums.bungie.org/story/?read=75036 and https://forums.bungie.org/story/?read=75037
Unlike the original log posts, a couple of them had to be split up into multiple parts as they were too long for a single story forum post. The final 2 levels of System Shock 2 and the final Marathon comparison list are the most annoying ones, where I had to make the conclusion chapter and its list a separate episode despite already doing that for the final boss.