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Group Policy preferences provide the means to simplify deployment and standardize configurations. They add to Group Policy a centralized system for deploying preferences (that is, settings that users can change later). You can also use Group Policy preferences to configure applications that are not Group Policy-aware. By using Group Policy preferences, you can change or delete almost any registry setting, file or folder shortcut and can manage local users and groups for any computer in the domain, and more. You are not limited by the contents of Administrative Template files. The Group Policy Management Editor (GPME) includes Group Policy preferences.
and lot more can be done using GP preferences.