I have only one complain about the issue tracker. When you create a pull request there should be a dropdown-autocomplete kind of thing so that I don't have to write down in a piece of paper which issues (i.e 'fixes #30 #120') are fixed in the branch I am about to merge.

The rest of it actually fits my needs although I am a one man army so YMMV.

We personally use JIRA with Bitbucket to handle our issues.

I'm a one-man show at the moment working on 3+ repositories on Bitbucket. I tried using JIRA for a few months late last year, and it wasn't a great experience or me, so I ended reverting back to using the Bitbucket issue tracker. If I get the time to write an issue exporter (or find one that works), I'll be migrating to Github or something with an issue tracker that gets attention.

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.

JIRA does allow you to link issues and create subtasks; you mentioned that you're experience wasn't that great with JIRA. Can you elaborate what problems you were facing?