I've just started using yEd and think it's (mostly) great (especially for the price).
However, I've found a couple of things really frustrating.
One is the use of 'unnatural' terms for things.
I guess there will be a huge impact on documentation etc. but it would be sooooooo much nicer if you called a diagram a diagram, rather than a graph. And as for "edges"? Really? An edge in everyone else's language is the line at the boundary of a shape. Other diagram apps call them "lines" or "connectors.
I don't know whether this started off as a 2nd language thing or a domain-specific language thing, and I know it's only really two words that I have to bend my head around each time, which isn't a lot, but it would be so much more obvious what was going on if you used the terms that most of your audience were familiar with.