I was thinking about how to extend this plugin and make it really flexible for when/if it gets included into the core.
Keeping the core up to date is vital, however, some larger/complex themes & plugins such as GeoTheme, WP E-Commerce etc, usually have a bit of a lead time before they release a version that is 100% compatible with the new core version.
If the automatic updater were to download a new core version before the major plugin/theme was also updated, that could of course screw up a website installation.
So, what about a feature that would allow you to select the core theme/plugin in the website to "track" during auto updating.
Only when the theme/plugin version has been updated and marked as compatible with the new core version, would the auto-updater update the core.
Day 1 WP 3.4.2 & GeoTheme 3.2.1 (Compat. up to WP 3.4.2)
Day 2 WP 3.5 released
Day 5 Geotheme 3.2.2 updated (Compat. up to WP 3.5)
Day 5 WP 3.5 updated
Of course not keeping the core up to date is bad but so is losing the functionality of a website.