The overall api is strange. The each loops are backwards from the spec (key, value) instead of (value, key) and there are instances where it is key, value in jquery, there are instances where method names just don't make sense (I'd expect something like size to be dimensions etc), getters and setters as the same method, way too much argument overloading, inconsistent approach (selector.action, but wrap is the opposite of how the rest of the lib works). There is no kind of inheritance for their plugin architecture.

These are just things off the top of my head. I feel like jQuery is the same as PHP when it comes to api, and I make a living doing PHP.