Something as simple as the ux being designed for gamepads made for a second tier gameplay experience on pc. You see this even to this day where bungie's marathon has auto-aim assist for a supposed "boomer shooter".
Also, and maybe more importantly, the dev shops then were smaller and were more self-critical about what is actually a good game? It was the early days of the video game industry exploring the medium before the ridiculously bloated budgets of today's AAAA? studios.
Lastly, I am very critical of today's world-building in games. We don't have storytellers any more, but something called "narrative designers". Those empty heads are hired to tell me what to think. It's absolutely soul crushing.
That said, there are still gems out there. I hesitate to mention them because ultimately art is subjective; but one that gave me an ice pick to the head (in a good way) is Death Stranding.