The UI and milestones, though, I think are good. JIRA is to me the king of clunky. I've used it in 3 projects over the years and evaluated it last year, and I've been pretty disappointed with it.
To borrow from another comment here, it has a bit of a Bugzilla feel, like it just grew and grew, and you have tons of fields and features, but they're poorly designed and put together. A bit of a mess, to put it bluntly. FogBugz has a similar feel to me.
I encourage you to check out JetBrains' YouTrack. I never used it in a project, but a couple days evaluating gave me a good impression. Good luck with your search.