Take for example the admin UI. When adding "Application Links" to link Jira and Confluence with each other, Jira has a nice tabbed interface allowing you to configure it easily, whereas in Confluence, you have to scroll down a long sidebar with dozens of options until you chance upon the required link. Had similar experiences configuring various other options at the filesystem level.
Jira configuration was more coherent, fault tolerant and failed gracefully. Confluence configuration on the other hand was messy in comparison.