Problems: The frequently-changing database schema in which the wiki information is stored makes it difficult to maintain data across upgrades (requiring conversion scripts), offers no easy backup functionality, makes it difficult to access the data with other tools, and is generally fragile.
Proposed solution: Let's create a standardized file format (probably something XML-ish) for storing the information contained in a wiki. All the text, revisions, meta-data, and so on would be stored in a well-defined format, so that, for example, upgrading the wiki software (from any version to any other--no need to do one at a time!) could be done by exporting the wiki into this format and then importing it into the new installation. The export format would be publishable and easier to use for other applications, would be a simple file system for which commonly-available backup tools could be used. A periodic export/import would serve to clean the database of any reference errors and fragmentation. Tools could be created to work with the new format to create subsets, mirrors, and so on.
I already have some idea of what is needed, but I solicit input.