Historically, when Windows upgraded, it carried all its baggage with it from the previous install (for better or for worse). Windows 10, however, seems to have deviated from this. Now if an application is deemed incompatible with the build being upgraded to, the application will simply not be present in the post-upgrade operating system. Windows should warn the user of this prior to upgrade and, if ignored, report this in a report file at C:\Windows\Panther named miglog.xml that the application was not migrated forward.
When first faced with this news, it is logical to assume that this is a complete disaster and poor choice. However, consider the upgrade process as a guardian of sorts. After the upgrade, Microsoft would like you to be able to log in to the system and actually use it to do work. If an application is going to break the installation, why migrate it? Also note that I did not state the data would not be migrated. No, it is kept (if it is stored appropriately) in the user profile.
This makes the maneuvering of application compatibility between the OS and third-party software both problematic and somewhat pragmatic: problematic in that a slow software developer of a key enterprise application can demonstrably keep an upgrade from moving forward without significant application shims or other tricks, pragmatic because either the software works and therefore is migrated during the upgrade process, or it doesn't work and won't be there to create a fuss later on for the user.
It is also worth noting that some older applications used to get away with hiding settings (or even data in the form of binary blobs, and so on) in the registry. This practice was never really a good one to follow and now it comes with a penalty. Areas of the registry managed by the OS tend to not keep custom key entries when the OS install is upgraded. Generally speaking, there is no guarantee that the oddball registry hacks from legacy or internal applications are going to migrate for you if they are in registry areas generally reserved for the operating system as a general rule. Your mileage may vary.