Being able to set deault values for labels would be a huge bonus. i tend to use internal, centred, fit to node, and cropping in every flowchart node I use and it would speed up my work if I didn't have to edit the preferences on each node. ( I don't in practice as I create copies of the common nodes with the desired settings and just copy them when I want to use them but this is still tedious as i have to do it each time I use yEd.
yEd is the best graph editor I have ever used despite the above gripe!!