I'd say what sets the good games from then apart are the ones which were, back then, innovative. Hexen might've been a fun game, as was Heretic, but it is Doom and Quake which were ahead of their time.

EDIT: I disagree games are no longer good. Slay The Spire is a brilliant combination of rogue and card game. Total War: Warhammer II is a good real-time RTS with a non-realtime map component. World of Warcraft was a good MMORPG, and it is from this millennium (2004).