And in moving things around and re-aliging you have to re-learn the whole diagram. If the frobnitz was always in the upper right part of the diagram and suddenly it's moved to the center left because everything lines up better that way, well maybe it's helpful to someone who is looking at the diagram for the first time but if you've been working with it for six months suddenly it looks like a completely different thing.

It's like an ugly UI. It may be ugly but the people who use it, know it. When you "clean it up" you've now disrupted their mental models and they have to re-learn it all over again.