Part of the OBIEE upgrade includes a migration of the OBIEE 11g artefacts. The migration script provided by Oracle upgrades and migrates the Web Catalog and the Repository. This script doesn't migrate WebLogic users.
In order to avoid manually recreating these users in the 12c environment, you can use the Migration facility in WebLogic to export the Users, Groups & Administration Roles from the Security Realm. This will also incorporate the assignment of Users to WebLogic groups and Administration Roles.
This is achieved by:
Once all users have been successfully migrated, remember to delete the BISystemUser account in the 12c environment as 12c does not support a BI System User.
I'm an Oracle Ace Associate and a certified OBIEE 11g implementation specialist.