Tools like Yeoman can help here, but they're also relatively obscure and there's a lot of yak shaving involved in getting them working correctly.
In a sense complaining about this the Node world is like asking fish how they can stand being wet all the time. It's just part of the terrain.
I'm not saying what Node is doing is fundamentally wrong, but that this almost absurd aversion to making decisions for users is sometimes a bad thing.
For example, I'd love to be able to declare dependencies for an NPM module that are open-eneded, like "any one of A, B, or C will do", but like it is with Ruby, Python, etc. you must declare all or none.
I'm not trying to restrict choice, just cover the base condition of when you don't care of providing a sane default.
To a degree Rails has this: The first thing I do in a new project is jettison all the garbage I don't want (see you later turbolinks) and drop in all the things I do want. It's actually just a few lines to manipulate, so I can hardly complain.
In the Node world there's a lot of hand-holding required to get even the most basic application up and running. I can see this getting cut down dramatically if you had things like "npm install express +extras" where there was some way of saying "plus whatever other stuff you think is a good idea", or even an "express-fully-loaded" version of the package that comes with a bunch of stuff out of the box.
I really like Gulp and when configured it gives you an amazing amount of control over your build process. Although the Rails Asset Pipeline system works as a pretty good default out-of-the-box they really should steal some ideas from Gulp on configurability for those occasions where you want to change the default behaviour.
Vinyl.fs (https://github.com/gulpjs/vinyl-fs) is an amazing thing that the Ruby world desperately needs.