Personally, whether I write or reread, I find myself adding comments to the text all the time. So I'd like to have this ability here.
It could start very simple. For instance, in WriteMonkey (that uses Markdown/Textile as well) any paragraph that starts with a double slash is a comment. It has different color and doesn't add to the word count.
Scrivener has something called annotations that doesn't add to the word count as well.
Of course, you could also go further. You could (optionally) show comments to the right from the text (a bit like, say, here: http://tsi.github.io/inlineDisqussions/ ), you could make all comments hidable/foldable, you could attach comments to highlighted portions of the main text etc.
Luiz Rocha commented
This is very nice to have. Commenting out text, that is not exported or copied through a special copy function.
I would suggest the ability to comment out blocks of texts and, the killer one that no one offers (not even Atom), the ability to make each line a single comment.
Ex: You have a list of all the topics. You paste it on Write than comment out each list item individually, so you can start writing below each one, using it as a structural reference that will not show in the final product.