Lastly I\'ve been feeling like jQuery is slowly becoming the defacto standard in JS libraries (I might be wrong!), or at least that is more active than the rest of the framework
I think you should. I use jquery religiously, and I'm not a Javascript Pro. It's ease of use I think, is one of the most powerful things about it.
As far as i know, Prototype and jQuery mostly overlap, except that jQuery focuses mainly on DOM manipulation, ajax, events, etc, and doesn't really have some of the capabilities that Prototype has, like classes, inheritance, etc. However, if you don't need these things, and only want a framework for cross browser DOM manip, ajax, events, etc, then I think jQuery is the way to go.