It's hard for me to say without watching the video, but my guess is that it's because jQuery doesn't offer all the features of most other libraries that make JavaScript programming easier. jQuery's purpose is to make DOM manipulation easier by simplifying addressing of elements via CSS selectors, and providing an easy framework for altering those elements. It offers some other feautes such as Ajax requests, basic event management, templating, and some other rudimentary functionality, but that's about it.

Other libraries such as Prototype, MooTools, Ext JS and Dojo provide loads of other functionality for creating objects, managing arrays & collections, manipulating strings, and doing all the other nitty gritty things that we as programmers expect to be able to do.

In short, jQuery lacks the tools that one would want for large scale JavaScript applications. It's pretty uncommon to find any very JavaScript heavy sites using jQuery, for this very reason. For example, Mint.com is built on YUI. Apple's MobileMe web service runs on SproutCore (Apple's main site uses Prototype).

At least, that's what I think he means.