This page recommends not using jQuery because it is a heavy library, and even the jQuery UI and jQuery Mobile versions present poor performance, and jQuery Mobile in particular imposes a lot of rigidity.
This page provides some reasons why you should not use jQuery Mobile (which has jQuery as a dependency) in mobile applications, among which being heavy, poorly performing, poorly documented and having many bugs, and according to the site the reason is because jQM is geared towards mobile websites and not applications. In the comments section some disagree with this non-recommendation.
I also remember reading something about jQuery handling click and not touch events, which would be best for mobile applications. Clicks have a delay of 300 milliseconds, which greatly impairs application responsiveness.