I was browsing the WordPress Trac tonight, and I saw a ticket to convert from Prototype to jQuery as the new JavaScript framework in the admin area for version 2.2.
As discussed with Matt, he would like to see the Admin area, in 2.2, using jQuery as the Javascript library running the frontend.
It is ticket #3824 if you’re following the changes. Download the bleeding-edge version from Subversion to see the changes as they roll it out.