The first feature regards the interface. I believe the window for "keeping remote directory up to date" should be resizable in order for one to watch better the list of files that are uploaded.
The second feature is also about auto update. There is an option to watch or not for subfolders. Perhaps it would be useful there if there was
1) a "level option" (e.g. to update the first level of subfolders but not subfolders of subfolders, etc)
2) an option to exclude some path from updates; e.g. watch for all subfolders or for the first three levels of subfolders, except for the "/uploads/images" directory, etc.
Both can be achieved using a file mask in transfer settings.