Another possibility might be just colloring variables and assignments (since thats where the scoping actually matters)

I was just thinking the same; when all my syntax highlighting in a region looks backwards, I normally assume I've got a mismatched quote just before it. I think I'd be thinking that with this all the time.

Subtle changes in the background colour would be a nice alternative.

It is a good idea indeed. I believe Notepad++ does background scope highlighting already, just not accurate enough for JavaScript specifically.

Exactly my thoughts, this could work really well if implemented properly.

Yes; highlight BG lighter grey. This would be an awesome plugin for ST.

Make the background color become less contrasting with the foreground color the more you nest. The larger the number of nested scopes, the harder it's going to be to read it anyway!

I'm actually serious by the way.