I would find it helpful if there was a way to exclude "from scheduled backups" a list of directories and/or files which are contained in the public_html dir or for that matter anywhere within your home directory.
This way for example, if I were to place a large video or other type of large file online then it won’t get backed up every night to the the Amazon S3 server saving S3 storage and bandwidth charges.
Note:
These exclude files/directories are applicable globally for all websites/subdomains included in the backups. If you want to exclude the files/directories for website specific then you need to create schedule different backups for each domain.