My problem with automated diagram layouts has always been that the algorithm doesn't understand the sensible or hierarchical relationship between the blocks in

My problem with automated diagram layouts has always been that the algorithm doesn't understand the sensible or hierarchical relationship between the blocks in my diagram, which isn't always the same as what the connectors are trying to show. The algorithm optimizes for the connectors (crossings), which certainly contributes to readability, but often at a cost to the overall readability of my diagram.