Why I never update:
-WordPress updates always BREAK some of my plugins or my theme or my customizations. That's dumb and unprofessional and unacceptable in a production environment. As a programmer, I would call that a bug. A very large bug.
How to fix that:
-restructure your app so there's better separation of your core from plugins and themes. Enable total plugin flexibility, but Don't allow any plugins to alter your core at all.
-explore and learn from the plugin architecture of other products.
-implement some kind of sandboxing or internal file-mirroring, so customizations can alter your core without altering your core.
-break your core files down into many more, smaller, and functionally isolated files, to minimize the impact of customizations.
-add a tag to all core files called "UserCustomized". Your updates would then skip those files, and/or Back them up and report file differences to the admin, so the admin can manually reapply the customizations.
-your updater would automatically reapply customizations after updating, at a line-by-line level. This would be facilitated by breaking your core down into more, smaller files.
-have stronger rules for certifying plugins, to ensure your updates don't break them.
Hope you can fix this.