Javascript is no longer just a client side language, and because jQuery is so DOM dependent, it is a terrible candidate to move to the server.
code quality – jQuery has a huge community and a low learning curve. This is a perfect storm for lots of poorly written open source plugins.
inefficiency – jQuery is easy to write inefficiently. For instance, using jQuery’s each instead of for loops is unnecessary and could have a performance impact in some cases. Lots of good info about this stuff at JSPerf
bloat – jQuery is a huge library. Much of the time, you’ll use a small subset of it’s features, and grab the whole library. There are some great alternatives that will give you subsets of the features, like zepto.js, and underscore.js – depending on your situation, you can save some bytes by choosing the right library for your needs.
