We are using Jira to create transparency to management in our Agile Development cycle. We find it overly cumbersome and burdensome on developers, scrum master, product owners... although the charts produced are liked by management.
What alternatives on the "Enterprise" level exist for aiding Agile Development without creating hurdles in productivity. Ideally it should be as elegant as Agile itself and allow developers to dance without stepping on the toes of product owners.
If you are interested in alternative tools, then PivotalTracker, Rally and VersionOne are good alternatives. PivotalTracker is good for self-organized small teams, Rally and VersionOne are better suitable for larger enterprises with several teams on board.
Said that, I still believe you can use JIRA very efficiently without adding an overhead into the process. In our team we use JIRA and GreenHopper and are very happy with that.