Agreed.
As stated before, coming from a Ruby on Rails background you can compare NPM Modules to Ruby Gems (libraries that have functions that you can execute). The hard part is learning those module’s functions to use them correctly.
When you scaffold with Ruby on Rails, there are MUCH LESS files and I feel it’s easier to understand.
Well… Ruby is “SUPPOSED” to be easier to understand (isn’t that what it’s known for? haha)
I do like MEAN stack mainly because it’s all JavaScript. And MongoDB is just so sexy looking 
I’ll keep reading up on the core modules functions (fs, eventemitters, callbacks, express), and hopefully start understanding how to “correctly” put a working application together…