I made some training software for Naval Nuclear Power school, when I worked at the Bettis Atomic Power Laboratory. The managers had selected Macromedia Authorware as the development platform long before I came on board. Mainly because it supposedly had a low learning curve and "anyone" could program just by dragging these pretty blocks out onto the canvas..
Sigh.. So I often got comments on how my lessons were so much better than other peoples lessons. And then other people were using my code snippets, etc. etc. And my "secret" was that I found that macromedia left hooks into the blocks so I could program with normal pseudo code logic to make the type of interaction happen that I wanted to make happen.
And that is what I would suggest. Allow for language support in each of your flow diagram blocks. That's where the power will come from.