I had to learn how to use gulp and npm and browserify and and and ohmygodthelistgoeson, and I tell you I feel exactly the opposite.
Trying to bolt tooling onto an existing project is daunting, especially when you're not sure how it works yet. When I started with a fresh skeleton project, two source files, the whole shebang set-up, it was super easy. Just add my extra source files in the dir, and it's picked up.
I love it when a skeleton project includes the entire toolset. I can easily remove stuff I don't need, even when I don't know how it works. But adding JS tooling myself? What a disaster.
Now, I look at my first project, the one I had to add gulp and everything to myself, and it's a complete mess. A lot of time and effort would have been saved if I had just started with a good directory structure right away.