According to Aaron Newton of Clientcide, this is not the question to be asking.

And I happen to agree with him.

These two frameworks just aren’t trying to do the same things. They overlap in the functionality they provide, but they are not trying to do the same things

Opposite Directions

MooTools is aimed more at JavaScript developers, while jQuery is more for people who want to implement JavaScript functionality in the easiest possible way.

jQuery is for people who aren’t necessarily interested in delving deep into JavaScript while MooTools provides an object-oriented framework for hardcore JavaScript development. This is why most people find MooTools harder to use in comparison to jQuery.

jQuery makes working with the DOM easier. MooTools makes working with all of the JavaScript language – not just the DOM – easier.

Both are fantastic libraries/frameworks and I think the better question for you to ask is

Which one should I use for this project

This can be determined by circumstances beyond your control e.g. The project leadership has already selected a framework for you, or the application development framework you are developing on is already using one over the other – and you may wish to avoid bloating-up your application with multiple libraries and increasing load times (not to mention script conflicts).

Different Camps

Here’s an example of what the world’s most popular PHP content frameworks have chosen:

Drupal - jQuery
WordPress - jQuery
Joomla – MooTools

I work in each of these environments and I recommend to anyone doing the same to view jQuery and MooTools as tools – not competitors. You might simple prefer the one over the other, at the end of the day they are just JavaScript; and there’s a right one (tool) for the job at hand.

The Real Thing

I also recommend learning pure JavaScript. It’ll give you a better understanding of what’s going on under the bonnet and you’ll find it easier to work with other JavaScript abstraction libraries. I’ve found my copy of JavaScript Bible – 6th Edition to be quite a handy mate for occasional reference.

How do you see this debate?

/* Update */

Aaron Newton authored the book:
MooTools Essentials: The Official MooTools Reference for JavaScript™ and Ajax Development

Read the full jQuery vs MooTools comparison  here