The addition of pull requests is a nice step in the right direction, but what would really set the Atlassian suite apart, and make my life a lot easier, would be to have really strong integration through the whole development cycle for a particular issue.

The biggest thing that's missing right now is the integration between pull requests and JIRA issues. In general, a pull request will probably be related to some particular issue. During development, there will be some comments relating to speccing out the issue and probably some code-review type comments on the pull request itself. It would be beyond convenient if all of those were connected into one discussion. There might be multiple pull requests involved in a single issue, and they should be linked with statuses on the issue itself.

It's a pain to have the discussion, code review, and resolution split between the issue and the pull request. They need to all be integrated together.