I was amazed at how rigid Jira is when I started using it (we used a heavily in-house customized version of Sabrina before, and Rally as well). Sure, if you have loads of time you can work with an admin to write custom code for it, but at the level of what one of many teams can do with it directly, it offers virtually no options.

You want to split stories and leave sub-tasks behind? Sorry, that's not Agile, so we're not going to make it easy.

You want to Subtask estimates to accrue to the Story estimate? Sorry, that's not Agile, so we're not going to make it easy.

You want to customize the sprint report based on custom labels? Nope, probably not Agile.

You want to plan the capacity of your team to see how much work you should take into an iteration taking into account vacations and partial availability? Sorry, that's not Agile, so we're not going to make it easy.

And on and on, with very basic needs...