The system that you mentioned in the orginial post looks pretty good as far as pre-builts go.
However, customization is the name of the game with the system I build. I don't put in features I don't need, and I don't leave out features I do need.
Also, a lot of times you don't actually get a copy of the OS when buying a pre-built system. Those system restore disks are really annoying, and they should actually give you a copy of the OS.
Furthermore, some forms of tweaking are not a possibility on pre-built systems. Options like bank interleave, command rate, pci bus mastering, and others are simply not available for tinkering on pre-built systems.
The lack of a quality PSU is another major downfall in purchasing pre-builts. Generic power supplies can leave users with unprecidented problems, especially when trying to add new components. Cheap memory is another area OEMs use to cut costs.
On that note, the support of the store is a good commodity to have. However, if you know what you're doing, you will be able to support yourself as competently as any Best Buy worker. All you need to work there is an A+ certification, which I got at the age of 14. For the basic user, this type of system should suffice. However, I would never buy a pre-built system under any circumstances. Plus, putting together a new system is fun!