When trying to register a plugin assembly containing custom workflow activities to CRM Online using the Plugin Registration Tool from the 2013 SDK, the custom workflow activities were not visible. Only plugins.
Tried changing the assembly major version, and the key which signs the assembly - no luck.
The solution was to use the Plugin Registration Tool from the pre-release 2015 SDK found here - http://www.microsoft.com/en-us/download/details.aspx?id=44567.