We use Jira for agile and this article is pretty spot on. We finally have it configured to fit our workflow, but, that took a while. Also; Atlassian likes to change the UI quite a bit in Jira (stop f*cking with it already!) so every week or so you get to learn something new.
In fact, we're considering rolling our own app to handle tickets/hours because of it.
I think you may have been caught up in a once-off UI rewrite over the last year. In general we don't change things that often, though there are minor improvements we try to roll out regularly.