It seems like one of the ironies of git-flow is that it would actually work better if you used it with Mercurial rather than Git, because Mercurial stores what branch you were on when you made a commit. This means that a tool could automatically look at the Mercurial commit tree and figure out which swimlane each commit belongs in, and use this information to draw a commit history tree that wasn't such a mess.

I apologize for the self-promotion, but this answer on Stack Overflow (and the question) talks about this difference between Git and Mercurial, and includes links to articles that explain it better than I could:

http://stackoverflow.com/a/26784550/1013442