Must keep up with OEM 12c Grid Control updates…
With the new release of Enterprise Manager, I upgraded my 12.1.0.3.0 installation successfully using the superb documentation here. It is however, important to note that the post-steps are also important. For example, upgrading (at the very least) the Management Agent on the OMS host, and de-installation of the old-OMS home. Gokhan Atil wrote a good post on the actual upgrade process which is available on his blog.
Management Agent Upgrade on the OMS Host:
The upgrade process for agents has not changed since EM’s previous 12c releases.
1. Navigate to the “Upgrade Agents” link under the Setup -> Manage Cloud Control menu.
2. Select the agent(s) for the OMS Hosts and click “OK”.
3. With the Agents selected, click on “Submit”. You have the option to override the “Privileged Credentials” to run the root.sh script.
4. The submitted job takes a few minutes before it completes (hopefully successfully!).
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Thoughts from James H. Lui 