For large UserFlows and flowparts I find myself printing and marking, commenting and coloring the design.
For example:
That could be a part of the userinterface.
It would be great to have the option to color elements of design screens.
For example when desiging a UserFlow it would be great to have the option to give any element (decision, flowpart, page) a color.
That could group elements that together perform one function, or mark elements that have been tested OK and untested elements.
Furthermore for large User Flows it would be nice to have the possibility to mark an area with a set of lines (or a square box) and then give that area a color.
The area would be behind the elements, and perhaps you can order different areas on top of each other (to indicate functions and subfunctions)
Each area could be given a visible title to clarify the name of a (sub)function in large UserFlows. (just like in the foto)
And I think it would look cool… 
(Could generate nice marketing pics!)