I've been asking myself this very same question for a while now, by means of just trying to wrap my head around the argument. And with ever discussion I read, the overwhelming response has been "More widely adopted - therefore better".
I am one who uses both extensively. JQuery at work (adopted because it was "more widely adopted") and Mootools on personal projects. As a result, I constantly find myself feeling crippled when using JQuery; Be it with JSON support, element creation, event handling... and so on. At work, I find myself writing chains 75 events long... and I feel dirty as a result.
My main overall beef with JQuery though, is that there's a lack of consistency or practice where plug-ins and 3rd party developers are concerned. The anecdotal "More plug-ins are available" really doesn't help me when there's no consistency between the plug-ins, structurally or otherwise. It took me several weeks to learn the "accepted" plug-in model, and even then, I've adapted my own pragmatic style into it, as I find error and inefficiency within the current structures. It can be said that it's a 'Pro' that anyone can jump in and start JQuerying it up. However, I am more inclined to call that a 'Con', in that you will see 30 different ways to accomplish something, and it's difficult to pin an accepted standard.
So what does it mean to "Know JQuery", Does it mean you know how to rock a little .hide().show().fadeIn().fadeOut()?
When I have to get gangster on my JS at work, I miss me some Mootools. I mean no Native JSON support? C'mon......
In response to the "Widely adopted" response, we all know OSCommerce is the most "Widely Adopted" shopping cart, and we all know what a pile of shit that is. I'm in no way comparing JQuery to OSCommerce. I'm simply pointing out the faulty of "Widely Adopted" response.
As for plugins, the App store for apple has what... 100k apps? 50,000 are fart apps. Sure there's a lot of plugins to JQuery, but the ratio of trash to worth-while is great.
