There is also anecdotal evidence that jQuery qua jQuery has some fundamental limits. I worked on a largish jQuery application, written by ninja badasses, and it creaked a lot more than it should have for its size.
Comparable systems built on YUI seemed to have more structure. I actually went through the exercise of converting a prototype from jQuery to YUI3, and spent a lot of time working out their respective "philosophies". (see http://jsrosettastone.com)
There are newer frameworks (eg JavelinJS) that aim to be to jQuery what jQuery was to other frameworks.