I've already posted this to the hackers ML, but I think there might be some people in these forums, who are interested in this, too.
I developed a management package for WordPress, which will perform backups and upgrades each with a single click. It is called WP-Manage. It is developed entirely in PHP and is an addon to WordPress. (Not a plugin, though, because it is not called by the WP plugin subsystem but it's rather WP-Manage to pull in WordPress.)
The Backup routine creates a MySQL dump of the WP tables, gathers all WP files and puts all this stuff into a nice zip file. The Upgrade routine downloads the latest WordPress, unpacks it, deletes the old files and inserts the new ones. All these actions don't require funky PHP extensions -- they are all handled by the WP-Manage package, together with some nice third-party-libs.
The backup and the upgrade routine are independent from each other, and it is to say that the upgrade feature might not be the right thing for every one. But e.g. if you installed WordPress for a friend or a customer with no knowledge of FTP, PHP and MySQL, you might find an ideal solution in this upgrade feature.
Documentation, screenshots and downloads are available at the WP-Manage homepage. Feedback is very apprechiated.