It would be great to have multiple "secondary" views of the same graph, with the possibility of defining an alternate node/edge layout for each view without altering the "base" view's layout.
I often use yEd to draw graphs whose nodes are positioned so that they match some underlying geographical base. For example, nodes may correspond to elements of a water supply network, with edges being water pipes. When nodes are positioned that way, however, the graph may become harder to work with, due to partially overlapping nodes or nodes that are too far apart. In this case, a secondary view that allows me to re-arrange the graph so that all nodes are equidistant, for example, would be very useful. I'd use the main view to get the final result, and the alternate view to define the graph topology more easily. Of course, the underlying model would be the same graph, and adding an edge to a node in the secondary view would automatically update the main view (and vice-versa).