I consider JIRA a code smell: if an organization uses it, I probably won't be satisfied working with them. I don't think it's because of anything especially bad with Atlassian (although I was furious when they removed the ability to edit Confluence in raw mode), as that the managers I least want to work for seem especially attracted to it.

Your comment just illuminated that for me and I think you're right. It's the micromanager's dream, but for good managers it doesn't seem to offer enough over the competition to draw them in. The best I've worked with considered PM tools essentially fungible, and therefore weren't likely to invest in 1) paying for the Atlassian suite or 2) the overhead of getting it up and running.