The release cycle for WordPress 3.6 isn’t going to start until January, but we can of course start to drop in some early things before then. (This worked out nicely before the start of 3.5.)
With that in mind, I have added jQuery 1.9 Beta 1 to trunk. It comes with a migration plugin for deprecated/removed features, and this migration plugin issues warnings in the console so we may fix them. Yes, we are likely to ship the migration plugin in 3.6 final; that’s why it exists. But for now, we should aim to fix anything not only outright broken in core, but also any warnings. (There are a lot of them.)
For more, see the jQuery announcement post and the WordPress core Trac ticket, #22975.
A side note: If you are using the WordPress Beta Tester plugin and wish to go back to the 3.5 branch, you can do so by changing the update stream setting from “Bleeding edge nightlies” (which is currently 3.6-alpha) to “Point release nightlies” (which is currently 3.5.1-alpha) and then downgrade. Of course, we’re happy to have you testing the 3.6 branch, which will be kept fairly stable throughout its development.