The Logging plugin should be modified such that it provides static methods that act as a service to other plugins, similar to how the Tld provides a service of sorts to the Url plugin. The Seen, Heard, Willsee, and Search features should be moved into separate plugins that pull from the Logging plugin. This will allow those features to be enabled or disabled individually.
Next, methods for querying the Logging plugin should allow for the optional specification of a channel by which to filter the results of the query so that they can be channel-specific if desired.
It may also be prudent to allow for configuration of what events Logging actually logs to the database. Though there is no obvious bug in the code, it appears that messages from the bot itself, such as posts with URL titles, aren't being logged.