Those are also completely different engine designs and purposes.
Well, you brought Quake into the discussion, not me.
The MW/Ob engines weren't designed to have parts of the game completely rewritten and replaced, because the engine wasn't designed for reuse. The Quake and Unreal engines were designed to be licensed to third parties, hence the need for easilly replacing some core game logic. The MW/Ob engines weren't designed for use outside of their respective games. Such a capability would be quite problematic, too... imagine you have a couple hundred mods, and the majority of them all have their own rewritten game.dll.
The "rewritten game.dll" problem is easily solvable: Allow multiple DLLs to be loaded, like UDK-based games do. There will still be conflicts, but we know how to deal with those from modding for Oblivion.
In general, Oblivion could use more of its inner workings moved from the engine code to modifiable scripts and configuration files. The hope is Skyrim does that (so we can, for example, more easily mod in additional skills, magical effects, or even add attributes back if we want to), but I won't hold my breath.