If you go to the jQuery site, here’s what it says at the top of the page:
And if you go to MooTools, this is what you’ll find:
Mootools has previously been known for its silky smooth effects and great DOM utilities, but they also have performance on their side as well. JQuery on the other hand has to have the friendliest syntax ever with chaining and selectors, with just enough effects to make you hungry for more. This makes the user frustrated. Just as you get comfortable with a framework something as disturbing as this test comes about.
JQuery focuses on expressiveness, quick and easy coding, and the DOM while MooTools focuses on extension, inheritance, legibility, reuse, and maintainability. If you put those two things on opposite sides of a scale, the jQuery side translates into something with which it’s easy to get started and see quick results but can turn into code that’s harder to reuse and maintain (but really that’s up to you; it’s not JQuery’s problem), while the MooTools side takes longer to learn and requires you to write more code upfront before you see results, but afterwards is more reusable and more maintainable.
Which one is better? We can’t really say. Both of them are excellent choices. They both have benefits. MooTools’ dynamic element creation and manipulation is better, but jQuery has a much larger and more active community. JQuery is easier to learn and the documentation is much better, but MooTools provides an inheritance mechanism which is very nice if you’re used to OOP. Both frameworks have their strengths and weaknesses, but, in general, they are both great choices.
Another good piece of information that may affect your choice is that Microsoft and Nokia are adopting jQuery and will be integrated in Visual Studio. However if you are using Aptana there is already support for most of the frameworks including Mootools.
If you look at the things JQuery can do, there’s often a counterpart in MooTools. If you look at the things MooTools can do, there is often no way to emulate it using jQuery code because of JQuery’s focus on the DOM. MooTools has a broader functionality than jQuery, but there’s nothing about jQuery that prevents you from doing those things.