Per http://confluence.atlassian.com/display/DOC/Global+Permissions+Overview#GlobalPermissionsOverview-ComparingtheAdministratorPermissionswiththeconfluenceadministratorsGroup and https://support.atlassian.com/browse/CSP-18893, even if a user or a group to which he belongs has System Administrator permissions, the user is in fact not a system administrator as he does not automatically have permissions on all wiki spaces.

Problem: In virtually all other products I've used, System Administrator literally means an "administrator" of the entire "system." Confluence has apparently created a new definition for System Administrator where you are an administrator of some things but not of others.

Preferred resolution: Give us the ability to apply an "administrator of the entire system" privilege to arbitrary accounts or groups. My Confluence install is integrated with Active Directory via LDAP, and we would institutionally prefer to use LDAP to assign permissions. Forcing us to use a local group runs contrary to a key benefit of LDAP integration.

If the preferred resolution is not possible, it would be good to either 1. clarify in the product that the privilege called System Administrator is not in fact a true system administrator privilege or 2. rename the privilege to something that couldn't be confused with a system administrator privilege.