Complexity doesn't have to be ugly: Glyphobet links to dburrows' diagrams of the apt system as an example of why automated graph drawing tools could benefit with interaction from skilled graphic designers.
Beyond Glyphobet's point (which I agree with) I think the drawings could also benefit from some of my own research, on confluent drawing. It's not that the drawing is nonplanar — one benefit of confluence is replacing many crossing single-to-single connections by a single many-to-many connection, reducing the number of crossings, but that isn't an issue in this drawing. Rather, what I think would most improve the drawings (beyond a little more care in vertex placement and edge routing so that unnecessary crossings and close pairs of edges are avoided) would be to replace groups of single-to-single connections, all with the same source or sink and all with the same label, by a single-to-many or many-to-single confluent connection with only one label. The label clutter is as big or bigger an issue in these drawings than the edge clutter, and confluence can help with that.