John Carmack wasn't wrong: Those games are still legends, and rightfully so. A focus on gameplay is a blessing and a curse: when you strip away all but the most basic context and themes, there's a certain sense of purity which, much like HL's innovations did for it, give a distinct feel to your games. OTOH, if you rely on gameplay and level design alone, your game lives and dies how how good that gameplay feels, how tight those mechanics are, and most of all, how solid the levels are. Doom, Quake, and Quake 3 all pulled it off. Doom 3 and Quake 4, ironically id's most story-focused games... didn't.
It may not be a coincedence that all but one of id's best games came before Romero left, and the other one was a pure multiplayer gameplay experience, rather than the standard story-driven affair.