I have a bit of trouble reading the skill tree. The biggest problem is definitely the fact that learned skills and skills with missing requirements look exactly the same. A nice, solidly shaded box might be nice. Or, skills that you can't yet learn could be a red or orange color? I'm not sure what, but it definitely needs to be distinguishable.
Also, and I'm not sure if there's anything to be done about it, but the mouseover of the skills can sometimes be rather slow in loading and moving over them to get to the middleish ones can sometimes load the wrong skill. I blame AJAX.