It's interesting to hear him say that npm and node_modules are regrets since lots of complaints about Go packaging from people new to Go ask for something similar...
I think the package system consists of many parts. Some parts of npm are much better than with most package systems, some really suck. Maybe if npm weren't included so deeply into Node, it would make something like Yarn emerge sooner and replace npm without much hassle.
I don't agree with those complaints, but I do agree with you that "some parts" are really good. node really figured out the right search strategy for an unscoped import. (e.g. "require 'foo';" rather than "require './bar/foo';") Just look for a directory with the name "node_modules". If you don't find it, go up one directory and try again. So simple! So predictable! So complete! It works so well, all manner of "left-pad" abominations can be supported. Any other system should think very carefully before using a different import search strategy.
[0] with the exception of those related to path depth: I think those are resolved now? I wouldn't know because I stay on an OS that doesn't go out of its way to frustrate me.