The one thing I really liked about cPanel (and not much else), was how it handled this particular issue. Upon creating a new site, you would assign a unique username to it, which would then be used everywhere: as the ssh/ftp login, database name and user prefix, directory name, shell user, etc. This makes for a very well organised and coherent system, easy to navigate through.
Would something like that not be possible with ispconfig as well? Assigning a unique (string) identifier to each client and website, to be used throughout the system?