Searching is a challenge in Confluence. If you know the Space (we group our functional areas into 'Spaces' in Confluence), then searching is straight-forward, but if you don't know the Space, the searching becomes a bit hit and miss.
Organizing child pages under a parent is tedious. Rather than allowing a drag-and-drop interface, you have to go into Space Tools, then navigate through to the parent page and manually re-sort pages. Once in the Tools area, the feature set is good, but it would be nice to have fewer clicks or some sort of toggle to Edit Mode which allowed these features while still on the Confluence Page.
When presenting Tables of JIRA
Issues meeting specific criterion, the refresh/load time can get very slow. If there were an option to either prioritize the load order or the option to run synchronously/asynchronously, it would be a better UX.
Adding Security to Pages/Spaces can be a challenge. The UI for this feature often simply tells you that the permissions are inherited, and you have to navigate up a level or three to find those specific 'inherited permissions'. Each page should have its own listing of permissions with some indication of whether they are inherited or not, with an option to edit on the page (not in the parent or grandparent, etc.).
In working with the underlying database content, there are some major drawbacks... First, the underlying data for the pages is a long string of html, so any sort of searching is impossible. The option (or a built-in mechanism) to segment out sections of a page in the database would help in this effort tremendously.
Second, the underlying database has no easy way to apply the same security placed on the pages (see two points above for Security UI issues). Because we cannot reliably determine access/permissions to the pages from the DB, we have locked down all DB tables to ensure that no sensitive information is viewable by unauthorized users.