I'm not even really sure the equivalent of what files would be left out of UBB.C for an upgrade; definately the vars_ files though.
That was the difference, we didn't want people over-writing their vars files and having snitty-fits
For minor upgrades like 6.5.1 to 6.5.2 or 6.7.2 to 6.7.3 it made sense to use the upgrade zip but for major jumps from 6.5 to 6.7.x you really need to use the full zip, except for the vars files. Upload the files, go to the admin panel and the upgrade process from there was pretty painless.
Please make sure you backup all vars files, but for sure vars_cats, config, forums, and mods - most likely you'll have to overwrite the vars_wordlets files. I can't remember how much CC kept in the ubb_upgrade.cgi file.
