Sure, those of us with the technical know-how can upload the zip and handle this on the server end, but I expect that we're in the minority. And it's a chore to have to do it this way even for us, especially because the same method/commands don't necessarily work in all of the various server environs that we use if we manage more than one instance of XF. Also, any mistakes in the process can be very painful.
So what I would propose would be a solution where we would only need to upload a single upgrade file, which would be properly extracted by XF itself in the upgrade process. Obviously, the option would still have to be there to upload individual files when/if needed, so two packages would have to be provided. But in the majority of cases, I expect that a single file could be used.