[jph]

We're in the same boat with component diagrams, where the layout engine is insufficient. What did you choose to do for alternatives?

[gregmac]

I found using groups, colors and direction hints gets mostly around the issues. Enough that the benefits outweigh the downsides of switching to something else (that doesn't get source control, requires separate edit/export steps etc).

   group sys { 
      one -down-> two
   }