Normally, I create a pull request using the server response from git on the command line - Bitbucket replies with a URL to create a PR. In fact I have a git alias, 'git gone', which pushes, parses the response looking for the URL and launches it in my browser.

Per-developer repos are definitely an anti-pattern for Bitbucket usage. They just don't work well; it's all too easy to have a half-dozen slightly different versions of a branch in different people's repositories. It's generally better to use your local repo for your personal branches, and use a single repo on Bitbucket for team interaction. There's definitely a risk of data loss if it's not otherwise backed up, of course.

My personal bugbears are mostly relating to Jira. It needs a better mechanism for integrating estimated & actual numbers for predicting velocity. The only mechanism it natively supports is story points, and it's not enough. You often want to break down stories, but the hierarchy really doesn't work well. You can't put numbers on a finer granularity than stories.

It also doesn't work at a higher level, when developing a road map. It's just kind of stuck in the middle.