Oh i understand a bit better now. Well, I am not qualifyed to say what is dificult to do for the Subsonci developer(s).
But from my experience in ASP.NET i guess it would be better to keep the functions with zip file like it is today. But maybe make it so that users can see the servers file structers and put the file wherever they want, and have Subsonic extract it there.
Some fancy drag and drop feature to from client to server file structure would be even more nice
Some might argue that this out of the scope of Subsonic. Im not sure yet if this function would be wort it... As you mention yourself usere can use FTP.
On a sidenote: To make transfers to FTP more easy i reccomend NetDrive or FTP Drive. It basicly maps a ftp directory as local drive / network drive respectivly. So have your "power users" install this and they can drop file to the servsers filestrucure without having to fire up the FTP client, login on and so forth.