At my company we've recently begun using the Scrum agile methodology, and we've found that JIRA is not suited to tracking work by iteration / sprint. While versions can be used as iterations, this is confusing because iterations are an orthogonal concept. A particular problem we have with using versions for this purpose is that versions are specific to a single project (as they should be). However, our teams often work on multiple projects, and we track work across all these projects. Another difference is we usually determine the end date of a version by the estimates for assigned issues, while for iterations it is the opposite - we determine the end date first and then determine which issues it can contain.

JIRA should allow iterations to be defined with a name, start date, and end date. Additionally, an iteration is not tied to one project, but may be assigned to any number of projects. Perhaps some sort of "iteration schedule" could be created, with projects assigned to an iteration schedule receiving all the iterations on that schedule. Alternatively, if sub-projects were supported (as per JRA-12241) an iteration created in a parent project could be inherited by the children.

Any relevant reports should be included, such as burndown charts. In addition to tracking by time, it would also be nice to track by story points.

Other functionality might be helpful. For example, at the end of a sprint I want to push any unfinished items to the next sprint. Items in progress need to be split, perhaps with separate subtasks automatically created?