I find my biggest problem with the tree is that I can select only one thing at a time. In such a complex view that holds visual organization, it blows my mind that the same simple "click->drag over area to select->BOOM selected!" functions of the windows desktop and other visual-organization-based-applications don't exist here.
Workflow in the tree is just soooo slow when it comes to having lots of splits and plugins all over. Make it easy to grab and move sections of plugins in the tree please!
Simple request that will make many lives easier - they just don't know it yet :)