If you are creating a backup as of x point in time, you should be backing up all files and folders, not just some. However if you are restricted on space you could actually exclude items such as admin, applications and system. But only do this if you ensure you make a full backup every time you upgrade, or add any applications/plugins (you should do this anyway)
The reason you could technically exclude those, is you could always just download a copy of them from your client area.