There is a little thing that's been bugging me for ages about this otherwise fantastic plugin. I have to ask clients not to update it because they will lose their custom toolbar and config settings.
The toolbar configuration is even editable from the plugin - so how difficult would it be to save these changes and preserve them across updates?
The other thing that we have changed in this plugin is the file ckeditor-for-wordpress/cdeditor/config.js - to add this setting -
config.baseHref = '/';
Again, it would be nice to preserve the contents of this file across updates.