I don't see how this could be implemented any time soon because it would require that everything involved be changed (BSP, compilers, the engine). Plus, it would be more fitting if it involved a new map file format, but regardless...
It would be great if you could paint a texture onto another brush like it was decal. This would have the advantage of adding extra features to a surface (windows, etc.) without raising the already-precious polygon count. For example, for a building, you could construct the actual brushes for windows on the first floor and then paint the window textures for the upper floors. No one would notice this and maps would look fantastic. To do this now, you would have to create a new repeating texture, but this would result in greater file size usage for the map.