I can't agree with you that FPSes haven't changed since then; it's only true if you are very selective about what you consider important about a FPS. What you have said implies that you don't care about story line, realism of physics simulation, gameplay, etc., which I'm quite certain is simply not objectively true of the gaming marketplace. Even if you think it's the "3D" that matters, then things were vastly better in Quake than Duke Nukem, where you could look directly up and down without bad distortion etc.
And then, one needs to ask, what quality is it of the 3D that matters? Simple things like decent texture scaling (trilinear filtered mipmapping, anisotropic filtering etc.) and antialiasing make a big difference, but are often only viable at high resolution in 6-month old games with the latest hardware, such are the demands of the processing.
Yeah, I found Portal by Valve Software a couple of years ago the same groundbreaking experience in terms of gameplay that I felt with those first 3D games. Some of my friends said the same about HalfLife before it.
For instance you couldn't do proper floors above floors, but there were some rendering tricks you could use to do bridges.
It also supported slanted floors, which helps level designers more than you realize. Also there were invisible teleports to fake a real 3d layout.
But the most important part was that the level designers were very good at using those tricks to hide the limits of the engine.
And they are still playable today. (At least if you substitute System Shock 2 for the original System Shock. The original's controls did not use the now-standard mouse-look.)
Halo later brought in regenerating health, but yeah, that's all I can think of.
And saying that, multiplayer in general seems like a big step (although not sure how well multiplayer was in the 90s)
Duke Nukem 3D brought the 3D into FPS. Because of this 3D, aiming with the mouse became the standard for generations of games. A few months later ID Software published Quake, which was also mind bending. I don't feel like FPS have evolved at all since that time. Better story lines, more guns and spells, more details in the physics engines, but the 3D is still the same for the vast majority of large studio productions.
This is why Duke Nukem is so mythical (and Quake 1), it set the foundation for modern FPS games. Over the time, people forgot about their 1996 experience but where kept on the bandwagon by "Duke Nukem Forever in the following year".
Now I'll agree that the probability that this game lives up its expectations tends toward zero but hey, its like a software game soap opera going on!