The Quake 3 engine added procedural curved surfaces which were computed on the CPU. Meanwhile, the Unreal engine simply optimized the rendering of arbitrary meshes which allowed artists to build any shaped surface they want and then let the GPU brute force it.
The Doom 3 engine added a unified lighting model based on stencil shadows. Again, this was a heavily CPU based technique while the industry was trending towards being CPU-bound. Additionally, the chosen lighting equations created a very plastic-like look. Competitors used shadow maps which are generated by the GPU and these are still the standard in speed and quality for most games today.
The latest engine he is working on is pushing "mega textures" which effectively emulate a hardware paging technique in software. "Mega textures" is the next logical step in mip-mapping, but mip-mapping has been performed by the graphics card for over a decade now. The SeaDragon team over at Microsoft Research and Live Labs built a superior version of this idea before Carmack started on this and are working actively with hardware vendors and the Direct3D team to speed it up for use in games.
Once again, Carmack has opted to trade precious CPU cycles -- better budgeted for game logic, physics, and AI -- for generality. He seems to be fighting a crusade against special cases in his engines at the expense of the games made with that engine.
There is a great reason why the Unreal Engine has been the most popular middleware platform since Quake 3...