A couple of people have actually put that idea on the WebAssist wish list.
I would recommend, however, not moving the folders in the meantime. I am a lot like you about trying to keep in neat and tidy, but I found this actually (if you're not super careful) will lead to more problems. It's also nice when you update a page such as a Universal Email page, it is easier just to find the one folder and send the update rather than navigate through a folder hierarchy.
But yes, I do, as well, think it would be cool if maybe all the WebAssist stuff in the future would get added to the "includes" directory.