I’ve made a list of all of the things in the codex that I think need to be updated for WordPress 3.5: https://make.wordpress.org/docs/2012/11/27/if-all-goes-to-plan-wordpress-3-5-will/
It’s in progress so please feel free to add to it.
But what’s most relevant, is that some of the updates will be relevant to the user manual too. We’re already aware of the updates to media, but there have been a number of changes to the Settings as well. I’m not sure if they were considered when we created the manual.