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.
You should consider Microsoft Team Foundation Server (TFS) with Microsoft Visual Studio Scrum 1.0 template and Urban Turtle add-on.
Urban Turtle add the right skin to turn TFS into Scrum. According to Microsoft, the premier Agile tooling for TFS is Urban Turtle. Discloser: I work with the Urban Turtle team. So do not take my words. Instead, read what Brian Harry, who is the Product Unit Manager for Team Foundation Server, said about Urban Turtle: "...awesome Scrum experience for TFS."
You can read Brian Harry's blog post here
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.
If you look for a simple tool specifically designed not to get in the way of Scrum teams consider Banana Scrum.
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