As is, yEd appears to be pretty powerful, supporting a wide range of formats, sophisticated graph arangement, extensive customization, etc.
I would love to use thes features to visualize pre-existing graphs. However yEd aways comes up as a graph editor, always ready to add some default new node or new edge. Ideally, in such modes one would still be able to remove nodes from a viewing area, rearrange nodes, etc; but no to add nodes or edges not in the graph to start with.
As it stands, yEd is good for creating and editing graphs, but for the types of graphs that arise "naturally" outside the yEd editor, it makes no sense to add/delete entities. It is for such use cases that this type of feature would be desirabe.