Hmm, the first thing that comes to mind, is that if you don't miss it, you don't need it. I don't know why you are looking for better use? Is it the price you paid for it?
CPanel is a great tool for a sysadmin and saves a lot of typing commands. On the other hand, it limits the freedom you have to do your own thing with the server. CPanel is mostly usefull, because you can delegate a lot of stuff to your customer or reseller.
By the way, I think the FileManager sucks for years already.