If you haven't yet, do flag this up with the Ninjas through Help > Send Feedback. (This is really the only way to help help it bubble up through the layers of priority in their database of issues to address).
I think, however, that they are unlikely to fix this family of bugs (unintelligible connector overlaps, spurious asymmetries etc) until version 6. It's rooted in the choice of Graphviz (which can't currently compute orthogonal allocations of space) as a layout engine. A solution would require extending Graphviz, adding a post-processor, or going for a different layout engine. (The last one seems unlikely).
It looks very much like a fudged compromise between those two perennial components of software engineering and perhaps human life in general – autonomous play and curiosity on the one hand (source of most creativity), and exchange of goods and services in a market on the other (source of most sustainability).
Graphviz has almost irresistible geek-cool, and plenty of scope for play and experimentation (I would have been tempted to choose it myself), but the market needed orthogonal trees, which Graphviz can't do. They clearly knew that orthogonal trees were important to customers – a noticeable proportion of the templates are for 'orgcharts', and until recently orgcharts were strongly foregrounded in the marketing. The compromise was to dress up non-orthogonal layouts in orthogonal connectors ...
(Probably looked OK in a few early test cases, but once you start to work with it, it's hard not to notice that you're looking at diagrams in drag – quite apart from the straightforward bugs ... )