Mootools isn't really used by Joomla on the frontend. It only really comes into play if you have an extension or feature that uses Mootools such as RokTabs, RokNavMenu or other plugins etc...
But in a default Joomla install, might as well disable it to reduce your load. It can be enabled or disable in the template manager.
You can load mootools 1.2 if you want but would probably break any JS extension you would use with Joomla

1. Since the backend requires Mootools 1.11 to run, I guess it loads when the url reads