I love the Compare Folder feature because it allows me to filter all the items that exist on both sides of the transfer, thus no need for "skipping" files that exist. But I think you could add something that would make it even more efficient and fast. Maybe adding another button, or just a setting in "Advanced" so that when you click "Compare Folder" it will filter the files/folders and then start transferring from the highlighted server to the other side. Maybe also a shortcut key to do this (Cntrl+Something).
Thanks for reading