I have been working with older versions (4, 5.x) of Jira before and recently switched to 6.2 OnDemand.
Before, I haven't used "stories" as explicit issue type and I only stumpled upon it when trying to work with the plan mode for scrum boards. It happens to be that by default, only stories can be estimated by story points, not new features etc.
Now I was wondering about when to use stories or new features or if I just should add story points as custom field to all issue types. I was searching for a reason why Atlassian implemented the specifics this way (how do they think it makes sense?) but it seems that in the overview of all issue types, stories are omitted. To me even more strange, when I try to access the help for the issues I see this:
Can someone bring a bit light in the dark of this new (?) feature?
As far as JIRA is considered 'Story' is yet another issue type. The reason why the story points makes sense at a Story level is because, a feature can be considered as a bigger piece of work which is not yet broken down to do an estimation.
Coming back to actual usage of JIRA Agile, you should consider using Epics rather than Features.
And JIRA agile also supports projections at an Epic level (Epic Charts)
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