Thief: The Dark Project / GOLD (1998 / 1999) - graphics is okay but character models are low polygonal it might put you off, Thief 2 was not so good and Thief 3 was almost broken, that last game in trilogy was made on Unreal Engine and there is no rope arrow mechanics among some other things, Thief (2014) is completely different game but in some way it could considered as a sequel to Thief 3 and it's better and still very different
System Shock 2 (1999) - probably the best Sci-Fi shooter with RPG elements, same engine as with Thief so same low poly models, Bioshock is crap in comparison but so many people love Bioshock, as for System Shock 1 it was a solid Sci-Fi game but still nothing spectacular, many old school fans prefer SS1 over SS2 which I just can't understand, original release had no option to redefine controls and was very clunky, I suggest to check Nightdive re-release with proper mouse look and fast paced engine (I beleive KEX was used there), I'm waiting for a sequel since for 22 years
Deus Ex (2000) - it was almost a masterpiece and the closest thing to Thief and System Shock 2, some of the key people worked on Thief 1, all other Deus Ex games are crap, except maybe for Mankind Divided but it was cut for several DLCs and there will be no sequel despite a cliffhanger ending for unknown reasons (the game was commercially successful even if barely).
Arx Fatalis (2002) - probably the best fantasy FPS with RPG elements in the world, the magic system was adapted from Ultima Underworld like some other elements but EA was not interested in another sequel so Arkane Studios had to make their own game, it's unusual, it's strange, it's brilliant
Prey (2017) - that's the closest thing to System Shock 2 from the creators of Arx Fatalis, there are some minor issues and you might not like it for a first few minutes but then it'll consume you, completely unrelated to original Prey (2006) game which is a solid FPS game with no sequel
And you've mentioned Clive Barker's Jericho, I did't like the game but there was another one called Clive Barker's Undying (2001), that game was the best dark FPS game I've ever played.