The favourites system (aka Navigation) works a bit more intuitively now, because Media Modes are now just shortcuts to places in the tree, so no more non-responsive favourites-menu clicks.
I agree with marko that the 'Organise' dialogue is clunky and unfriendly. (I also think that it, along with other dialogues such as 'Import', would be much improved if you could resize them). Version 11.1.97 still does that multiple flash/refresh when you click 'up' or 'down', and still with the same scroll-bar position problem.
I'm with hit_ny too on the folder suggestion. It would be much more useful and usable if it functioned like a web-browser favourites menu.
Personally, I'd like it if any navigation entries (like 'back', 'refresh', etc.) that I have included in my toolbar were automatically removed from the navigation menu; it's practically never going to be handier for me to go 'back' by either clicking on the Navigation toolbar icon and choosing it from the drop-down or by right-clicking on a tree-item and choosing it from the Navigation sub-menu, than it is to use the dedicated toolbar icon. Those Navigation-menu entries clutter and elongate the favourites system; though that really wouldn't matter if there was a folder system in place.