yWorks employee here, though not working on yEd. Thanks for the kind words.
As for your wish, I think that's already there. You can select many items at once and change them all in the same way, e.g. changing the label font. To select all elements of the same type, simply select one of them (e.g. a label (you may have to use Ctrl+click to select a label on top of a node)) and press Ctrl+A. That should select all labels, while not selecting anything else. From there you can change properties for all of them at once. I think we've added this to yEd Live (the online version) as well recently.
There is also a powerful selection dialog under Tools > Select elements where you can basically select everything that matches certain criteria, such as all nodes with the same color, or predecessors of the currently selected node. Afterwards you can change properties in the panel as usual. This one only exists in the desktop version, though.
As for your wish, I think that's already there. You can select many items at once and change them all in the same way, e.g. changing the label font. To select all elements of the same type, simply select one of them (e.g. a label (you may have to use Ctrl+click to select a label on top of a node)) and press Ctrl+A. That should select all labels, while not selecting anything else. From there you can change properties for all of them at once. I think we've added this to yEd Live (the online version) as well recently.
There is also a powerful selection dialog under Tools > Select elements where you can basically select everything that matches certain criteria, such as all nodes with the same color, or predecessors of the currently selected node. Afterwards you can change properties in the panel as usual. This one only exists in the desktop version, though.