I wish they would add the ability to fast-forward merge from pull requests. I know many large projects (including Django) accept pull requests but don't merge them on Github simply because of the mess it makes of the history.
In my team's projects, code review in PRs made a mess of the history (certain devs in particular :P). We switched to a squash merge based workflow to address it, git reflow is our particular poison: https://github.com/reenhanced/gitreflow