The second would be the overuse of build scripts in that the build seems more complicated than the app in both time to get the thing up and complicated chaining steps. I've not had much fun debugging grunt, gulp or webpack in some of these fortune 1000 projects and I have a hard time wanting to give a shit about knowing them in great detail as the app should be the focus.
The parts of node that I most like are the core libraries that come with the install. When I try to stick with those as much as possible rather than using some half-baked npm module for every whim, I have a very pleasurable experience.
The async/wait and promises, etc along with piping streams are quite elegant in how modules can be snapped together like lego pieces but I find that people fuck it up terribly when they half know it as I initially did and it becomes akin to the messiness of es5 callbacks.
It does take some time to really utilize async well so I would recommend to read up on those concepts in great detail prior to jumping in.
Please npm responsibly.