As of 15.08.2016 GitHub allows changing the target branch of a pull request via the GUI. Click Edit
next to the title, then select the branch from the dropdown.
You can now change the base branch of an open pull request. After you’ve created a pull request, you can modify the base branch so that the changes in the pull request are compared against a different branch. By changing the base branch of your original pull request rather than opening a new one with the correct base branch, you’ll be able to keep valuable work and discussion.