[kazinator]

In cases when the boxes overlap, there are ways to choose an arrow which will not cross the boxes. But this is prevented by the constraint that the starting and ending points must be on the midpoint of a box edge. If the midpoint of the a given edge is occluded by a box, or occludes a box, then that edge is not considered, even though it is partially visible and has a viable point for the arrow.

E.g. if we could start an arrow in the middle of the small protruding "ledge" of the bottom box, we could do this:

    ,-------.
   :         :
   :         v
   : +----------------+
   : |                |
  +----------------+  |
  |                |--+
  |                |
  +----------------+

It's not written in stone that box-and-arrow diagrams must be connected by edge midpoints. That can't even work well any time you have multiple arrows emanating or terminating on the same edge.

Very good first iteration round, though.

[Akronymus]

So, you could take the midpoint of non overlapped edge segments? And split that segment as more arrows leave from it? Sounds like a good further step.

Another one would be reducing the amount of crossover between different arrows.