Some kind of mechanism to deal with configuration and plugin versioning. For instance it could be that the workflow bundle was made with the WSDL activity for Taverna 2.2 - but in Taverna 2.4 there's a new property "port" in addition to "wsdl" and "methodname". The configuration could then be upgraded, but only if "port" is optional or have a default value. On the other side, a configuration with the "port" property defined can't be downgraded to work with 2.2 - and so it should not be included when the default value is used.
This issue must also deal with how plugin versions can be represented, version ranges would be good. It's unclear whether plugin and activity would have the same version number, and if this version would match the POM/OSGibundle version or match the official Taverna release version - but remember it should also work for third-party activities