It's true that our community could use a renewed focus around best practices, and it's true that the stack itself is way more complicated than it needs to be. In that sense, I don't disagree with the point of this article at all, but it's important to remember that when things grow organically they will tend to get messy, and the alternative (somehow structured growth, governing bodies, etc) is far worse.
I fail to see the "many excellent options". Awful ones are, on the other hand, abundant.
And even those that are decent have the other issues the article mentions: they are short-lived, with developers soon moving to the next shiny thing etc.
I've been loosely following a lot of projects for several years now... it's hard to even keep a broad awareness at this point. That doesn't even count the platform/systems tooling that I'd honestly rather not think about...
Chef, Puppet, now Ansible... Hadoop, MongoDB, RethinkDB, Cassandra, ElasticSearch, Redis, Couch, etc... Hapi, Express, Koa ... NGINX, HTTP2/SPDY, Varnish, etc... Cloud-VMs, Azure, Amazon, Rackspace, Joyent, Linode, Digital Ocean... OpenStack, Varnish, Docker ...
It goes on, and on... there's too much to keep up with awareness of... let alone what needs to be dug into at this point. It's honestly a bit overwhelming. I just want to get back to whelmed...
I'd really like to be doing more time coding, which right now, I'm spending more time on platform stuff... evaluating packages in npm/github isn't so bad.. much more than that, it gets interesting.
Javascript is definitely in danger. I feel like its just hurtling down a trajectory of becoming the assembly of the web. The library churn is not helping.
IMHO that's the best possible thing which could happen to it. JavaScript is a hideous, ugly, horrible, broken language. But so is machine code, and it doesn't matter because I can write in real languages and let a Sufficiently Intelligent Compiler™ figure out how to encode my program. If I could write in a real language and have it compiled to JavaScript, I'd be a lot happier about writing browser-based apps.
(I'm still not happy about every single web page demanding executable code in order to, e.g., display a blog entry, but that's a different issue)
I think a good attempt at providing a "3000 ft survey of the JS landscape" is http://alpha.ideavis.co/529cc5f
I'd love to see an automated tool that could aggregate stats from a range of JavaScript repositories (e.g. GitHub, NPM, Bower) into something like Dustin's graphic.