The problem is the import of "Vmware Update Manager" data. In my case i did this to bypass it:
1- I reverted all the changes that the upgrade process did: From the ESXi hosting the new and old Appliance, I removed the new appliance and powered up the old one again. Thats important for the next steps to work properly.
2- Wait till the old vCenter Appliance is fully functional again and ensure that the Update Manager plugin is working correctly (start the "update manager" service in the update manager machine if the "Migration Assistant" stopped it, which was my case). Also in my case, after login on the old appliance with vsphere client, the upgrade process left an orphaned new appliance, you can delete it safely.
3- Once the update manager is working again, Uninstall the "vmware vsphere update manager" from "ADD/Remove programs" at the Update manager machine. If it's the update manager 6 update2 it will also unregister the plugin in the old vsphere appliance. Can't say about different versions because 6update2 was my scenario.
4- If the plugin uninstalled correctly you should not see the plugin at vsphere client anymore. Check it after restarting vsphre client on your computer and if it's gone then you can proceed with the upgrade/migration again, now without "migration assistant" for update manager because we removed it completely.
That did the trick for me, if uninstalling the update manager software don't uninstall the plugin for you, then you should remove it manually from the old vsphere appliance (there are guides on how to unregister plugins in vcenter 6), and start the upgrade to 6.5 process without it on your environment.
In my case I wanted to migrate Update Manager just to not configure it again, no critical data lost because everything can be downloaded again, but If you have complex configurations/baselines that must be exported/imported then I suppose you'll need to wait until vmWare releases a fix to that problem.
regards and profit.
Ezequiel