Yes, it's questionable as to the direction taken regarding BioShock coming from the group who developed System Shock 2. BioShock feels watered down in comparison, a SS2 for dummies if you will. The atmosphere and the level of customization found in SS2 I think given the time it was released set it apart from almost everything else, as far as single player FPS games from that time are concerned. Unlike SS2, once you beat BioShock, there's really little reason to go through again, not to mention no MP as is found in SS2 too. It's a refined game and one I enjoyed the majority of my playthrough of, but it's not my favourite or the FPS that sticks with me all these years.
Not to say all homage should be paid to the firestarter, but Quake in it's refinement of multi-player from Doom and Doom 2 in addition to providing a (then) truly awe inspiring actual 3D world for me sets it apart from the all the rest. It could be argued that without Hovertank 3-D there is no Wolf3D and without Wolf3D there is no Doom and without Doom there is no Quake. For me, there is no modern genre of FPS games without Quake.
As for GoldenEye 64, it could be said to be the turning point and genesis of all modern console FPS games. I've never owned a Nintendo 64 and with regards to the people I hung out with back in GoldenEyes heyday I was essentially the only person without the means to play it. As such my memories of GoldenEye consist of frustration and lack of involvement thanks to unfamiliarity with the N64 and in general non-keyboard based FPS controls. I remain sour to this day but I have lightened my attitude to the undeniable impact it had on the industry, and for that it does have my respect. This despite I have a huge inclination against playing console FPS games to this day (see: exclusion Metroid Prime 1 & 2). Keyboard+mouse or bust.