It is certainly isn't obvious to me. NPM is the best package manager I have used for a specific language. I do think there are things that can be improved, like everything else, but overall I think it is pretty good. And the vast majority of complaints I have seen are just nitpicks. So yes I would be very curious to know what you think is so obviously broken with it.
While I don't hate npm, there are better examples of how to do package management. For example, Nuget gets a lot of things right with no nested dependencies.