Online WYSIWYG editors have improved considerably since they first came out. They are getting aligned with the best practices of Web publishing. However, a problem still hovers around them, which is not their own fault.
When WYSIWYG editors are allowed to be used, most users assume that they can copy-paste across various WYSIWYG editors. For example, many users type in Microsoft Word, copy from it and paste into the online WYSIWYG editor. Sometimes they have a part copied from other softwares like email clients. These softwares usually inject a lot of cruft and proprietary code into the markup. While it might not be visible through the browser, this affects usually causes inconsistencies, invalidates the page, and affects performance and the SEO. I was surprised to know that, for many users, being able to copy-paste from word processors was the biggest incentive for using the online WYSIWYG editors. No wonder, the alternatives have not been popular with the non-techie users. Some online WYSIWYG editors are trying to solve this by cleaning up the code, however, there are too many possible variations that happen across different versions of different WYSIWYG editors. It will be a continuous challenge to attend to.
I think the core problem is in the way we treat them. As the online editors are getting better at the Web, they are lesser about visual formatting and more about using the right markup and style elements. We have to educate the user about this and about the possible dangers of copy and paste. We can start by calling them something else. I thought WYSIWYM was a great alternative. However, only better tools, or better documentation will not help us. We need a community effort to increase awareness about using the online editors. We have to help improve creating content on the Web through online editors or it will soon become a thorn in the flesh.