I suppose the idea would be that there would be a basic template that most mod creators could copy/paste with all the basic stuff (basic code, project files, etc.) so they wouldn't have to do that, similar to universal (only actually used regularily)
This would be a scripting method, only each mod would be separated. Could you imagine a hundred different versions of ScriptDev2 being worked on by a hundred different people? Adding and removing patches would be hell. It's easier to keep it separated, and it would allow for more advanced things (loading/unloading mods on demand)
I like cipherCOM's system, but it is very complicated, and maybe needlessly. I don't see why using script hooks similar to the AI now wouldn't work with some sort of mod class to manage mods loading/unloading and calling the mod functions.