andrew - i remember there was some concern about confusing admins on ability to only add system roles or something like that?
need to keep in mind that you cannot associate a user with a Role; you can associate a user with a Role on a certain object. in the "system permissions" dialog (available via the "Configure" section), it is fairly clear that the "certain object" is "System". The main goal of the "Add User(s)" dialog is to add user(s) to the system in general, without permissions in mind. We can add an option within the "Add User(s)" dialog to associate these newly-added users with system permissions, but it should be very clear that these are *system* permissions. BTW, the appropriate location for adding the "add system permissions" action is the permissions sub-tab in the users main tab (see bug 650915), however it won't allow you deal with multiple users at once - only with the user selected in the main grid (on which we are showing the sub-tab details).
since request here is about system permissions, closing as duplicate. *** This bug has been marked as a duplicate of bug 650915 ***