I agree with Ryan. The tree seems to give a much better overview, plus there's a much higher level of familiarity for people coming from glassfish 1-2.x so you'll probably have to field far fewer support questions on the move of properties.
I don't disagree with JPTech that the menu's are more 'logical' but I still prefer the tree because of its 'conceptual' presentation. I think most of the people who are drawn to a gui are so because of it's conceptual design which I read as 'intuitiveness'.
Andrew
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