What separates Doom or Half Life mods from Skyrim and Minecraft mods in my mind is that Doom and Half Life mods are mostly new levels that aren't connected to the original game. Mods for open world games change the original experience, while mods for linear shooters create new experiences. They're both modding communities, but they aren't that comparable in their focus.

There are Half Life mods that change the original campaign and there are Skyrim mods that are disconnected from the original game, but they're not where most of the community focuses their energy or what most people play.