A lot of JIRA plugins leave a lot of cruft behind when uninstalling and removing them from a particular JIRA instance. A lot of the reason for this is because a plugin can only be disabled or uninstalled and a plugin is unable to determine which method you have selected. In fact a plugin uninstall really only performs the plugin disable feature in addition to removing the plugin .JAR file from the server file system.
Most JIRA plugins will not remove data on a plugin disable/uninstall because administrators may be required to disable plugins to diagnose performance issues with their particular JIRA instance. You wouldn't want to have all of your data wiped out in a production environment!
With the Root Cause Analysis plugin, we have strived to ensure that we remove as much of the data that the plugin produced during its tenure as possible.