Material related to my thesis Difﬁculties maintaining separation of structure and presentation while using a browser based WYSIWYG-editor can be found here. More material (such as the project files for the LyX-editor with which it was written) is available upon request.
Further research on the subject has been done. In a nutshell the best solution seems to be using some kind of simplified markup such as Textile or Markdown accompanied with a WYSIWYG-like toolbar for inserting code snippets, so that the user doesn't need to remember them. This gives the user a clear view of whatever markup is within the editable content, and no invisible markup is left polluting the page (potentially causing unexpected behavior).
Difﬁculties maintaining separation of structure and presentation while using a browser based WYSIWYG-editor by Simon Rönnqvist is licensed under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License.
Permissions beyond the scope of this license may be available at http://simon.fi/contact.