I like yEd's speed for large graphs, but it's often useful to hide a subset of the graph based on a set of filter criteria in custom properties.
I'd like to see a feature implemented, similar to the "selection" tool, that allows filtering of nodes and edges (inclusively or exclusively) on a set of criteria that acts on custom properties.
This feature wouldn't affect the underlying data in the graph, just the visual and the layout (i.e. layout algorithms would arrange as if the nodes not currently visible don't exist).
The ability to save the filter criteria for quick access to pick different views would also be good.