Promoting other new web standards than ES6 could also be beneficial. Atom already use flexbox, because it gives us functionality which didn't exist before. Why not using Web Components? It gives us the feature to scope stylesheets. This is something really important, if you want to safely extend the GUI.
I do understand the benefits for using CSON. JSON is very limited - mainly because it doesn't support comments. But why shouldn't Atom prefer JSON5, which is a little bit more standard-orientated?
Speaking about standard-orientated: Maybe rework would be a good alternative to Less? It would fit the idea to work with modern web technologies like ES6 or Web Components, because you can forward polyfill some newish CSS specs. It also integrates very nicely with npm packaging!
I have no problem supporting CS (or TypeScript or something else) at all. But I would do it the other way around. Instead of making every example in the docs in CS/CSON and noting that JS/JSON could be used, too, in the last paragraph, make JS/JSON the default language - and note that you can use other languages like CS/CSON, too. JS will always be the common denominator.
Please consider using more standard-orientated and future-orientated technologies in all docs and modules (be it a core module or something else).