I did an upgrade like this less than a month ago, you read all about it in this post 12600 with VSX low on memory.
One is now with CPUSE and one is clean install, first thing I ran into is that the upgraded machine has an issue with the cluster state of the management interface. Second issue I found was that CCP was set to broadcast on the upgraded system but was set to auto on the clean install, ending up in broadcast/unicast setting.
VS0 is acting up due to the Cluster interface mis-configuration, state is active/down.
Identity Awareness is not working from a VS when it is running on the clean install system, the AD account gets locked within minutes. Move the IA using VS to the upgraded system and reset the lock and IA works just fine.
My customer is not really happy to execute the recommendation from TAC, to do a clean install (for the interface issues) on the other machine as well, as they fear that IA won't work at all anymore.
So it really depends, a clean install will set all R80.20 defaults, that are done below the VSX reconfiguration levels. An upgrade will keep the system as is, which in some cases is what you want/need.