Real bundling with tools like Browserify is making it more and more feasible to use single-purpose libraries instead of monolithic ones like jQuery.
I agree with all those things. jQuery is the lowest common denominator. It's the best at nothing, bloated with support for Palm Pilot browsers and Safari 1.0, and doesn't have all the cool grunt/gulp/amd/broccoli/cucumber/jsx/fotm neologisms. If I'm building a new, long-term project, I'm going to evaluate all the options, and craft the best possible technology stack for my new app.
But sometimes worse is better. Like a smooth pebble pulled out of a stream, it's taken a long journey and had most of the rough edges rubbed off. It's already in your browser cache from 4 different CDNs. Someone else can pick it up and support it easily. And that's what often makes it the best choice, when you want to avoid bikeshedding over what the hottest new thing is, and just make a webpage.
jQuery may not be the best technology, but it's a sane default.
Thankfully we only support IE9+ where I work, so I grab the latest 2.x version these days.
[0] - http://blog.jquery.com/2013/04/18/jquery-2-0-released/