Sorry, I don't agree. On the one hand, they might be more precisely in positioning nodes. But on the other hand, they are cumbersome in their usage.
You need a lot of clicking to use the alignment tools (Edit -> Align Nodes -> Choose one) and not all of their keybindings are usable, for Strg + Alt + Left or Right are already in usage of the gnome desktop environment and their derivates. The other possibilty you suggested is keying in the precise coordinates in the properties view. This is not practical too. Just imagine you have a big drawing with lets say 100 nodes and you want to replace many of the a bit. At some point of time this will become unhandy.
I'm pretty sure you heard it many times before and I'm afraid you got really tired of it. But nevertheless it is true. yEd is in competition with MS Visio and Visio is in the matter of user experience better. You know, in the past I used Visio a lot but unfortunately the company has limited buying Visio licenses, so many of us are now looking for a new tool as a substitution. Other small things would also be good, for they would make yEd more intuitive in usage. For example scrolling instead of zooming with the mouse wheel. Or scrolling right or left, up or down the drawing when placing the mouse on the horizontal or vertical scroll bar and scrolling the wheel. It would make the usability of the yEd much better.