Actually that's not correct when using node/npm (or anything else in the ecosystem like browserify). That is one of the impressive things about this platform: any number of different versions of the same module can be required by the same app. It would be nuts to do that in your own code, but as long as the craziness is in your dependencies it really doesn't matter.
Only one buggy implementation per project. Compare this to including the same library in dozen different versions, because dependencies have their own dependencies. And you can neither track the versions nor update them.
Using multiple versions of the same library is code smell. It's a stability issue, a security issue, a complexity-breeder, and an absolute nightmare for packagers.
And npm allows it to happen silently.
Actually though you're just talking about some bugs in X, or possibly some design flaws in Y. Passing [EDIT, because bare objects are fine:] class instances around like that is the real code smell. So much coupling, so little cohesion. We call them "modules" because we like modularity.
There is no clean way of packaging a typical node application.
Passing class instances around like that is the real code smell.
Often, yes, but not always. Allowing fine-grained control over performance is one good reason that a library might expose class instances from one of its dependencies.
A distro that still packages python 2 (i.e. all of them) has a particular "velocity", and therefore it has no business packaging Node or anything written in it. Maybe a distro could package TJ's "n" tool (helpfully, that's written in bash rather than node), which would actually be handy for distro users who also use Node, but that's it.
For example, you can install Wordpress on Arch with `pacman -S wordpress' and you'll have a managed wordpress installation in /usr/share/webapps/wordpress. Then you just edit some wordpress config files, set up your http server to serve php from that directory, and you have a wordpress blog.
It would be nice to be able to do the same with Ghost.
I'm sure if I look hard enough there are some silly idiosyncratic steps one might take to install this module. Suffice it to say that it's not installing the "npm way", so it's misguided to blame npm for packaging difficulties.
More generally, I can certainly understand distro packagers' refusal to recreate towering pyramids of node dependencies in their own package system. Some lines have to be drawn somewhere, and "major" modules must bundle many of their dependencies when packaged for distros. If module maintainers don't do this, and distro packagers can't, then the modules can't be packaged.
If there is a security fix, you should bump your dependency by hand, the other problems that you pointed out do not exist in Node (and it's about time they disappear in Java)
If its just a few lines of code, just copy the thing into your code base? throw a comment in saying "came from xxxx" so anyone reading your code knows that it might look like a overly generic function because it is.