Joomla is slowly switching from Mootools to JQuery. As many things depend on this it is a gradual process. The Joomla article manager has always used Mootools, as a result F2C has had to use it too. In Joomla 3.3 Mootools is still loaded by default. You can use different plugins to remove Mootools but than the F2C frond-end (based on Joomla Article Manager) no longer works. To allow Mootools just being loaded for F2C and other extensions which might require it you the following extension.

http://digitaldisseny.com/en/joomla-extensions/disable-mootools-joomla-per-itemid-solve-jquery-conflicts

As soon as JAM works with JQuery we will update F2C too, leaving Mootools behind at last.