The Phillies are willingly doing what they're doing. The best way to rebuild is to be absolutely terrible and build up your farm system for several years.
The Phillies got bad in the first place because they gave out bad contracts that nobody wanted to Halladay, Lee, Howard, Utley, Rollins, Ruiz, etc.. They paid older guys who they had no business paying, they wound up maxing out their payroll, and then went into a long, slow decline as their old players got older, more unmovable, and they couldn't get anything out of their depleted farm system.
When it's time for the Pirates to rebuild, they are going to be bad for several years. Ideally you time it so that you don't wallow in mediocrity for several years like the Phillies did under Ruben Amaro, Jr. They're going to tank, and tank hard. That old guy will be here for a year or two at the end of the window and then probably another 1-3 years afterwards -- years when the Pirates will assuredly be bad.