yEd uses Java's metallic theme by default. What you want is Java's GTKLookandFeel theme. Normally you would be able to do this by starting yEd with:
java -Dswing.defaultlaf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel -jar yed.jar
Due to a bug in yEd/Java this does not work currently. For now you will have to apply the
1.) Navigate to yEd's installation folder
2.) Edit yed.jar and delete the class causing the theme issues
mv yed.jar yed.zip
zip -d yed com/jgoodies/looks/plastic/Plastic3DLookAndFeel.class
mv yed.zip yed.jar
You can now start yEd in GTK mode.
With some Java versions you might run into a scenario where all fonts in the GTK theme are formatted in bold. You can troubleshoot this by uninstalling a korean font package:
sudo apt-get remove --purge fonts-unfonts-core
If you don't feel like removing packages just to troubleshoot Oracle's bugs you can try out the workaround outlined in this comment.