Some of the nifty features that I was referring to are the selection buttons. So in case you're not sure on which interface to use, I suggest you go with Commander first. Putting that aside, the fact that Total Commander proved once and for all that double panel file management IS superior, WinSCP's Explorer view is missing some really useful buttons from the handy-dandy toolbar.
You may then use drag and drop between Explorer and WinSCP. Alternatively you can go wild and have WinSCP desguise itself as Windows Explorer window! Ooh! Yeah, it's actually not that sweet. You can choose the rather standard commander type interface with two screens, one focusing on your local drives, the other on the remote storage. WinSCP greets you with the option of running it in two modes. Of course, you can't have much to improve when the main function is to transfer files, but some small features may go a long way in helping you accomplish this with ease. While still looking for an alternative to FileZilla, WinSCP appeared to be shinier.