Here's a simple reason why Moodle should adopt jQuery. According to the linked report, 60.4% of web sites use jQuery and the next highest total is none at 35.9%. Of the other proposed libraries that I remember being suggested, AngularJS is at 0.1% and EmberJS doesn't even rate.
Now, I'm not saying popularity is everything, but we should consider that it might be in Moodle's best interests to embrace the overwhelmingly most popular Javascript library simply because it is overwhelmingly popular. There are people who want to work on Moodle, and chances are that if they know any Javascript library, then they know and use jQuery. Thus, if Moodle uses jQuery, it is easier for those people to make new things for Moodle and I think that's something that we all want. That, in and of itself, is something that Moodle needs. Moodle needs happy and productive developers, not just for the PHP core, but also for the plugin ecosystem, theme development, and UI work.
Sure, there may come a day when jQuery development stops or jQuery is relegated to the 0.7% market share of YUI, and we'll have to consider what to do next. However, that's life. Changes come and go and we adapt to them. For now, by adopting jQuery we would be making a lot of people who already work on the fringes of Moodle happy, while getting the advantage of a Javascript framework that a lot of people actually like to work with.
Personally, I think there'd have to be some very persuasive arguments to convince me that going with jQuery is not the best short and long term decision to make right now. I'm prepared to listen to them, but I haven't seen anything that convinces me that jQuery would be a bad choice in this thread, yet. Furthermore, to me the suggestion that we should develop a Moodle specific javscript library instead of using jQuery (or something else) is a non-starter. Even though I've re-invented the wheel many times before, I am generally of the opinion that it is not a productive use of time and energy. That's particularly true if we're going to make a wheel that only fits on our own car, because more often than not when we're done we find that our new square shaped wheels don't work quite as well as we expected them to, and nobody has the the time to sand all the corners down.
Note: Some people have mentioned that there are some bad jQuery plugins among the 2576 plugins in jQuery's official repository and I'm sure they're correct, but I also know there are also some bad plugins among the 899 plugins in Moodle's official registery.