I'm not sure what you mean by "integrates terribly into the system." You can use cpanel to within minutes, upgrade perl, apache, php... you can install perl modules, ruby modules, handle all your dns, all your email accounts, set up name servers, all your domains, set up and configure a software firewall, install a dozen or more popular php based applications (several dozen if you have fantastico deluxe plugin).... run security checks and get advice about security settings... all your routine server functions can be done in seconds with cpanel with virtually no technical knowledge and without ever having to log in to the shell.

In fact, installing ffmpeg, mencoder, etc. was the only thing in over a year that I could not do with cpanel. I think its an awesome control panel. And as you mentioned, it comes standard with the ability to run suphp which to me is a major security blanket.

But each to his own I suppose... I'd trade it for your technical prowess :)