Probably the only ongoing issue I have with the node ecosystem (other than the general poor taste of JS developers, which is forgivable) is everything around versioning.
I don't understand how npm ended up the way it has--Bundler got it right, other people got it right...why isn't this a solved problem?
I know they're making it better, but then they go and do something like making a for-profit company out of it and I get nervous again.
Hell, package management in Elixir (http://hex.pm) works great.