Allow upgrades to be done via GUI. This would hopefully alleviate the permissions-based issues we've been seeing, and make upgrading easier in general, where people don't have to ssh/CLI things. The GUI upgrade path should work somewhat like the following: 

1. On the Site Administrator's System Information page, the Site Admin has the option to check for updates. If there is an update, they should also have the option of a) downloading the new package for a manual upgrade; or b) upgrading automatically via the GUI. 

2. Clicking the Automatic Upgrade button will prompt the user to back up their entire system using the backup plugin (see Bug 4846). 

3. After backup has been completed (or skipped!?), the system should download the new files and extract them, or maybe patch is the way to go. I'm a little fuzzy here. 

4. After files have been updated, the DB should be updated. 

Users should see visual confirmation of which steps have been accomplished.

We should take a look at what's happening in Wordpress under the hood when they do this, as it's very quick and painless*. Here's the automatic upgrade plugin that I believe was the foundation for what is now core functionality: http://wordpress.org/extend/plugins/wordpress-automatic-upgrade/. 

* I say quick and painless: it's always worked perfectly for me, in under 2 seconds. I've seen threads online while looking for more WP upgrade info that suggests this isn't always the case. For that reason, I'd suggest considering creating this as a plugin available from the plugin gallery first, allowing users to install and test at their own risk before moving into CVS.