Well.... Kinda what you talked about, Implementing the atmos script.
Except that i'd suggest improvement on modding without typing values as far as possible.
Suggestion 2. Adding new shader options. There's way to few for there to be any creativity involved anymore. If you've seen 5 you've seen them all.
Also i'd like to point out that there's no way there's going to be changes in the gameplay and such. It would mess up too much and is a big risk.