We personally use JIRA with Bitbucket to handle our issues.
The problem with the issue tracker on Bitbucket is that it's not getting better because it would 'cannibalise JIRA' sales, but it's ridiculous that in 2015 I still can't create links between issues, or create subtasks. If I had to pay for a better issue tracker that's built-in to Bitbucket (no JIRA), I'd pay it.