Adding an Overide Folder
That way we can Modify Various Scripts and facilitate Mod Distribution by simply placing files in the Overide Folder instead of rewriting the "Stock" files. Mod uninstall and exchange would also benefit from such a functionality.
I've never used it before, but isn't that what the -mod command switch does?

And of course I back the idea of scripting. Simply for a savegame to save the fact that it is running the script is plenty, it doesn't need to remember where it is in that script (those this would of course be excellent)