Sorry Irrational, but I prefer Looking Glass's Prequel.
SHODAN was way more interesting in her natural element: In control. She also didn't sound like a total ☺☺☺☺☺ who constantly hurled insults at you. On the contrary she even complimented you! (case in point: "Nice jump"). Foiling all her carefully laid plans backed up by plans until taking her down in cyberspace was very satisfying. The gameplay was also more of a straight shooter like BioShock. While I love System Shock 2 for many things, it's range of Sci-fi weaponry and gunplay was a disappointment in comparison.
System Shock 2 definitely is more scarier though thanks to the lack of ammo, breaking weapons and psychic monkeys.