I posted with out seeing your previous comment.
I've been thinking about this for the last couple of years. I think that the first few paragraphs from here sums it pretty well:
jqueryvsmootools.com/
The Mottos Say It All
If you go to the jQuery site, here's what it says at the top of the page:
jQuery is a fast and concise JavaScript Library that simplifies HTML document traversing, event handling, animating, and Ajax interactions for rapid web development. jQuery is designed to change the way that you write JavaScript.
...and if you go to MooTools, this is what you'll find:
MooTools is a compact, modular, Object-Oriented JavaScript framework designed for the intermediate to advanced JavaScript developer. It allows you to write powerful, flexible, and cross-browser code with its elegant, well documented, and coherent API.
I think this really sums it up. If you ask me (and you're reading this, so I'll assume you just have), the question isn't about which framework is better or worse. It's which one of these things above do you want to do? 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.
jQuery's description of itself talks about HTML, events, animations, Ajax, and web development. MooTools talks about object oriented-ness and writing powerful and flexible code. jQuery aspires to "change the way you write JavaScript" while MooTools is designed for the intermediate to advanced JavaScript developer.
Part of this consideration is the notion of a framework vs a toolkit. MooTools is a framework that attempts to implement JavaScript as it should be (according to MooTools' authors). The aim is to implement an API that feels like JavaScript and enhances everything; not just the DOM. jQuery is a toolkit that gives you an easy to use collection of methods in a self-contained system designed to make the DOM itself more pleasant. It just so happens that the DOM is where most people focus their effort when writing JavaScript, so in many cases, jQuery is all you need.
Most of the code you write when you write MooTools still feels like JavaScript. If you aren't interested in JavaScript as a language, then learning MooTools is going to feel like a chore. If you are interested in JavaScript and what makes it interesting, powerful, and expressive, then, personally, I think MooTools is the better choice.
That is why I'm not sure that I'll move to jquery, but we'll see
Cheers,
Daniel