Aaron Newton has written up what appears to be one of the most comprehensive and unbiased answers to the eternal question: jquery or mootools. I cannot recommend it enough to anyone that’s just starting with javascript or is looking at both frameworks from the “which is better for me and my project’s needs” angle. It’s worth mentioning before you begin, this is a comparison of the core functionality, provided by each framework – not what is possible should you decide to build on it.
The short summary: both frameworks are great but serve a different purpose, with jquery is more user and beginner-friendly, focused / optimised around DOM access and mootools, building and extending the javascript native prototypes and methods (not at the expense of the things that jquery can do).
Another way to look at it: mootools takes things further than jquery and makes javascript fun, introduces features that are coming in javascript 1.8 and provides a great layer for object orientated programming whereas jquery is staying where it’s at its best: shortcuts, chaining and styling, leaving anything else you may need to plugins and vanilla javascript.
The comments are also well worth the read, some good points on the pro’s and con’s of each framework and a bit on why mootools does not try to be unobtrusive / conflict free with other frameworks.
GitHub flavoured markdown enabled.