It bothers me that the graphviz algorithms almost always feel to me doing a poor job of laying out nodes. Like here in the neato layout you have both nodes overlapping eachother and edges overlapping with nodes, both which should be avoidable, and in fdp there is also some overlap and additionally RI and WA placements are "wrong" (non-planar). sfdp is just a mess, and twopi is even worse. Is there any software that works better?

I realize that this might be fundamentally difficult problem, but it just feels odd that there hasn't been much improvement in this area.