Scenario One: 11.2.4 (Patched) to 11.2.5
This scenario is beyond repair unless you wipe everything under \Oracle\Middleware, except for the sole exception of \Oracle\Middleware\user_projects\epmsystem1. Then bring over the Middleware folder from a fresh 11.2.5 install (from a throwaway VM sandbox for example).
As previously discussed on this blog and others on the Internet, when you apply the quarterly Oracle Critical Patch Update ("CPU") for Oracle Fusion Middleware, the WebLogic Server patch requires an update to the OPatch utility that cannot be rolled back at this time. This botches the entire in-place upgrade to 11.2.5 because you will be unable to redeploy any of the WebLogic Managed Servers.
Scenario Two: 11.2.4 (Not Patched) to 11.2.5
This in-place upgrade went flawlessly.
Scenario Three: 220.127.116.11.7xx to 11.2.5
Seriously, don't attempt this even though Oracle's 11.2.5 README says this upgrade path is certified. It is possible to repair it if you know the back-end Middleware folder structure extremely well. But you will spend waaaay more time repairing the system than if you used the swing server approach instead: Build a fresh 18.104.22.168 system in a VM, with its own database server, patch it up to 22.214.171.124.7xx to exactly match your PROD system, then perform an in-place upgrade to 126.96.36.199, and finally LCM your stuff out and import it into a fresh 11.2.5 system.
Why the in-place upgrade from 188.8.131.52/184.108.40.206 to 11.2.5 is fraught with danger:
Your Oracle HTTP Server ("OHS") folder structure now contains a mixture of OHS 220.127.116.11 and OHS 12c binaries. OHS refuses to start and you end up spending a lot of time troubleshooting until you discover the error messages (if you run launch.exe from the command line so you may see the error messages) really mean you're deep in what many IT professions call "DLL Hell".
Your domains\EPMSystem\bin folder scripts still refer to Java 6, JRockit 6, or Java 7 depending upon the state of your 11.1.2.x system. The WebLogic Managed Servers won't start.
Not trusting the upgrade, I blew away everything except for user_projects\epmsystem1, and then re-ran installTool and had it install 11.2.5 fresh. I then ran configTool and told it to re-use all of my databases, so that the application and Shared Services content was preserved. I then redeployed everything. This approach worked and all services, save one, are functional.
I'm still struggling on what to do with the old Reporting & Analysis Framework content. It did not get converted over to Document Repository and I don't see any back-end utilities that handle this. Perhaps I'm just overlooking something.
Because of this issue, Document Repository isn't visible in the Shared Services Console. We also get that odd error message about missing the default document when logging in to EPM Workspace. If you've encountered this issue have have overcome it, please let me know in the comments! This one will need to become an Oracle SR.
I could of course reconfigure Financial Reporting and tell it to drop & recreate the database, but then I lose all of my old RA Framework content. I can't "just LCM it over from the old system" because the customer's RAF repository is too huge to LCM. I've asked the customer for their assistance in cleaning up old PDFs from years past that aren't needed anymore. I'd then have to break up the LCM into smaller chunks and pray that 11.2.5 recognizes the content.... I suspect some Notepad++ trickery will be needed to do recursive find-replace operations.